Doctor Albert W. Wily/Archie Comics

This article is about Doctor Albert W. Wily as he appears in the Archie Comics Mega Man series.

Early Work
In the past, Dr. Wily was banned from directly working on advanced robotics, due to his creation of the Wily Walker and its equipment with dangerous chemical weapons. However, Wily convinced his colleague Dr. Thomas Light to let him help in the design and development of other highly advanced robots. He was thus involved in the creation of Blues, Dr. Light's first Robot Master. He also appears to have had a hand in the creation of the Sniper Joes, less-advanced robots based on Blues' design.

Let the Games Begin!
However, Wily eventually grew jealous of Dr. Light, and in Let the Games Begin! he stole six of Light's completed Robot Masters-Bomb Man, Guts Man, Cut Man, Elec Man, Fire Man, and Ice Man-and used them in an effort to establish himself as a dictator. He set the six robots on a rampage alongside Fleas and Sniper Joes, less-advanced machines he had managed to acquire, but was surprised when Dr. Light dispatched his robot son Rock, who had recently been rebuilt as Mega Man. As Wily observed, Mega Man defeated the Robot Masters one after another before being sent to Wily's base to apprehend the evil doctor. Undeterred, Wily dispatched his lesser minions to recover the defeated Robot Masters and repairs them, also sending his Yellow Devil to attack Mega Man.

After the Yellow Devil's defeat and Mega Man's success in tricking the Robot Masters into fighting each other as to whether or not to continue serving Wily, the doctor unleashed his latest creation: the evil Copy Robot, a clone of Mega Man. However, this machine was then destroyed by the Robot Masters, allowing Mega Man to face Wily one-on-one. Piloting his Wily Machine 1, Wily attempted to get Mega Man to surrender by taunting him, but ended up being defeated. Unfortunately for Mega Man, the captured Wily had a backup plan: Robot Masters Time Man and Oil Man.

Time Keeps Slipping
Wily was imprisoned for his crimes, and was soon scheduled to be relocated; unfortunately, he was able to signal Time Man and Oil Man with a Blader that entered his cell. On his orders, Time Man and several lesser robots attacked the convoy transferring him, with Time Man using his powers to free the doctor. Oil Man, meanwhile, was tasked with kidnapping Roll, Mega Man's sister, as insurance against anyone attempting to recapture him. Wily soon arrived at his new lair, and Roll was brought there as well, though Time Man and Oil Man's bickering annoyed their master. Despite his threat to dismantle Roll, Mega Man and the other Light Robot Masters began investigating, and teamed up with federal agent Roslyn Krantz. They soon learned the location of Wily's new lair-an old workshop where Wily's current pair of minions had been tested-and made their way there to confront him.

Time Man and Oil Man defeated the other six Robot Masters, and Wily soon had them under his control again-or so it seemed. Exulting in his apparent victory-achieved due to completing Oil Man and Time Man when Dr. Light felt they were too powered up to use-Wily called upon Mega Man and Krantz to surrender. His plans quickly fell apart when, during the ensuing battle, the other six Robot Masters revealed that Dr. Light had taken precautions against Wily reprogramming them again. Wily attempted to stop Agent Krantz from rescuing Roll, but she disabled the turret on his Wily Saucer. Unfortunately, the doctor had the last laugh, as it was revealed that he had controlled the saucer remotely and used a hologram to create the illusion of his presence. Despite the defeat, Wily remained determined, constructing a new base and beginning work on a new set of Robot Masters to prove his superiority to Dr. Light, and also ominously stated that he fully intends to take into account Mega Man into his plans.

The Return of Doctor Wily
Wily soon deployed his new group of Robot Masters, with Quick Man going to Light Labs to inform Dr. Light and Mega Man of this development. With the other seven-Wood Man, Bubble Man, Heat Man, Metal Man, Crash Man, and Flash Man-hidden around the city at strategic points with orders to attack six hours from the time Quick Man delivered his message or if the authorities were contacted, Mega Man was forced to challenge Wily's new Masters alone. The doctor refused Quick Man's offer to eliminate Mega Man, confident that he would achieve victory whether Mega Man won or lost. His reasoning soon became clear: each of the eight new Robot Masters had been equipped with part of a virus designed to reprogram Mega Man into serving Dr. Wily (something he had earlier hinted at in the ending of the Time Keeps Slipping arc). The task complete-and all his Robot Masters destroyed-Wily welcomed his new servant and repaired the damage he had suffered, fitting him with a purple scarf in the process. An unpleasant surprise soon arrived in the form of the eight Robot Masters loyal to Dr. Light, who came to rescue Mega Man from Wily's clutches. Undaunted, Wily deployed his Mecha Dragon to attack them, and soon deployed Mega Man as well. Unfortunately, this proved to be his undoing, as the Robot Masters supplied Mega Man with the last of the anti-virus code Dr. Light had attempted to upload to Mega Man during his battles with Wily's Masters. Wily's further defenses-the Guts Tank and Boobeam Trap-proved ineffective against the restored Mega Man and his allies. Wily confronted Mega Man himself in his Wily Machine 2, but it proved no match for the Metal Blade. Using holographic technology, Wily "transformed" into an Alien and continued the battle, but Mega Man soon discovered that his foe was up to his old tricks. Wily proved resourceful as ever, activating his castle's self-destruct and escaping through a hidden passage. His third plan thwarted, Wily decided to make his way towards the Lanfront Ruins in the Amazon Area.

Spiritus Ex Machina
Having heard of the EM Field emanating from the Lanfront Ruins, Wily set out to crack the mystery of its source. Eventually entering the Temple of the Moon, he fell into a hidden chamber where he discovered Ra Moon, an alien computer of immense power. Attempting to analyze it with his laptop computer, Wily was astonished as it used its cables to seize his device. Using the information contained therein, Ra Moon not only recreated his destroyed Robot Masters, but also gave life to several that Wily had previously designed in conjunction with Dr. Light. Exploring the ruins with Heat Man and Quick Man, he came across an ancient alien robot, whom he redesigned and had Ra Moon repair. This robot became Shadow Man, and joined the ranks of Wily's newest Robot Masters: Magnet Man, Snake Man, Hard Man, Top Man, Needle Man, Gemini Man, and Spark Man.

With the Temple of the Moon serving as his new lair, Wily was surprised when a proximity alarm he had set up went off. To his delight, the culprit is none other than Blues, who had run away from Dr. Light some time previously. After learning from Ra Moon that Blues' comatose state was due to the EM Field, which Ra Moon had the ability to extend over a greater area, Wily set about repairing the robot. With Blues restored and equipped with a new power core and weaponry, Wily was surprised to learn that Blues had left previously under the impression that Dr. Light intended to alter him. Wishing to serve Wily out of gratitude, Blues shunned his former name, also rejecting Proto Man when Wily suggested it. Given a shield and helmet, he accepted Wily's subsequent suggestion of Break Man, and joined Wily's large force of Robot Masters.

Rock of Ages
At some unknown point in the future, Wily invaded the Chronos Institute seeking the means to Time travel. His Genesis Unit and Mega Man Killers overwhelmed Time Man, the only visible defender, and used the technology in the institute and warp time, allowing them to turn it into the Wily Tower. Wily then began his trip through time, heading into the future in order to team up with a future version of himself, whom he felt confident would have already taken over the world. The energy from his craft affected Mega Man as well, and the Blue Bomber encountered Wily at an earlier point in time-specifically, during a battle with Ra Moon that was implied to have already transpired by that time. Yet another past version of Wily appeared to battle Mega Man at the helm of Gamma before Mega Man succeeded in returning himself to the present.

Meeting Ivo Robotnik
Wily met Ivo-better known as Dr. Eggman-after Flash Man brought him a blue gemstone found during his patrol of the Lanfront Ruins. Ignoring Ra Moon's appeal to be allowed to examine the gem, Wily plugged it into one of his own computers. As a result, the computer's signal managed to cross dimensional barriers to meet that of a computer in the jewel's home universe, the signal being a transmission sent by Dr. Eggman to various lieutenants. Thinking Wily had pirated his signal, Eggman accosted him, and the irate Wily claimed to be the greatest robotics genius on Earth. Hearing the name of Wily's home intrigued Eggman, and he soon realized that he was communicating with another dimension and was able to bring Wily up to speed on the concept. The two soon discovered much in common, and used the power of the Chaos Emerald-the jewel Flash Man had found-to create a pocket dimension between their two universes where they could meet. After an initial dispute on what to name it-Wily favoring "Skull Secret Zone" and Eggman "Egg Pocket Zone"-they agreed upon the name Skull Egg Zone.

Breaking Point
Some time later, Dr. Wily observed the renaming of Mega City in honor of Mega Man on television, and drew Break Man's attention to it. As he hoped, Break Man left in anger to disrupt the event. Glad that Break Man-who had been demonstrating a strong sense of morality-was occupied, Wily anticipated the fulfillment of the plan concocted by himself and his new partner Ivo. After watching some of the ensuing battle between Break Man and Mega Man, he departed through an Interdimensional Gateway to meet with Ivo and enact their plans.

Utilizing the altered laws of physics in the zone-which caused time to move differently there than in the doctors' home universes-they combined resources to construct a massive flying fortress. Once again bickering on a name-this time between "Death Egg Mark III" or "Wily Flying Fortress"-the two compromised again and dubbed it the Wily Egg. The two then used the power of the Chaos Emerald to fire the Genesis Wave, which altered both their universes, and retained their memories of the original and current timelines due to being in the Skull Egg Zone. This also ended up disrupting the battle between Mega Man and Break Man.

Worlds Collide
Eager to put his new knowledge to use, Wily immediately began planning to recreate all of his Robot Masters. Eggman supported the plan, but also suggested a further combination of their ideas: the Roboticized Masters.

Dispatching Bass, an elite creation of Wily's from his future, and Metal Sonic, Eggman's top robot enforcer, the pair kidnapped Tails, the sidekick of Eggman's nemesis Sonic the Hedgehog. By modifying Eggman's Roboticizer device with Robot Master technology, the two transformed Tails into Tails Man. Wily was initially disappointed by his lack of a personality, but soon cheered up as Eggman helped him see the potential of capturing more of Sonic's friends to acquire the remaining Chaos Emeralds. To that end, the pair sent Bass and Metal Sonic to capture Shadow the Hedgehog, Knuckles the Echidna, and Amy Rose, who became a new Shadow Man (not to be confused with the original), Knuckles Man, and Rose Woman. The quartet of Robot Masters were sent to Mega City after the gray Chaos Emerald, only to run afoul of Proto Man, who in this altered reality had broken ties with Wily.

The Roboticized Masters proved more than a match for Proto Man, who was fortunate enough to have Mega Man come to his aid. At the same time, Wily had a resurrected Copy Robot capture more of Sonic's allies: Vector the Crocodile, Espio the Chameleon, Charmy Bee, and Silver the Hedgehog. All four were taken for conversion into Roboticized Masters as well, and Sonic-witnessing Copy Robot's attack on Silver-gave chase to the Mega Man clone. In Mega City, Metal Sonic attacked Mega Man at such speed that his true appearance was impossible to determine, and then joined the Roboticized Masters in passing through a Warp Ring into the Green Hill Zone of their native world. Mega Man gave chase, continuing to follow Metal Sonic as the Roboticized Masters scattered, and was led right into Sonic. Thanks to Copy Robot and Metal Sonic's timing, the blue heroes mistakenly believed each other to be their previous quarry, and began battling.

Wily and Eggman-courtesy of Tails Man's camera work-watched with delight as their two nemeses battled each other, hoping that the two heroes would destroy one another. Thoroughly enjoying themselves-and being pampered by Eggman's assistants Orbot and Cubot-the pair received even more good news when Shadow Man, Knuckles Man, and Rose Woman arrived with the Chaos Emerald they had retrieved. With only one more Emerald left to complete their master plan, the pair agreed to wait until the second one arrived, wanting to put the last two in together and continue enjoying the fight. However, an unpleasant surprise occurred as the Warp Ring reopened, allowing Mega Man to travel back to Mega City with Sonic and Tails Man in pursuit. Realizing that only Dr. Light could be responsible, he informed Eggman about his old rival, whom they agreed needed to be dealt with. Bass then volunteered himself and Metal Sonic for the task, allowing Wily and Eggman to observe the continuing battle.

Sadly, the doctors' fun was short-lived, as a concerned Mega Man tried opening up dialogue with Sonic so as to avoid any harm to Mega City civilians. As the two heroes started to clear up the misunderstanding between them, Eggman ordered Tails Man to attack, and soon persuaded Wily to go along with it upon realizing that unless the heroes were destroyed they would team up. Tails Man ended up being restored to normal instead, with Mega Man acquiring his Tail Wind Master Weapon. However, the doctors enjoyed a small victory, as Dr. Light was brought back to the Wily Egg by Bass and Metal Sonic. The pair then observed a party of heroes-Mega Man, his dog Rush, Sonic, Tails, and a repaired Proto Man-as they entered the Skull Egg Zone. They dispatched Copy Robot, BusterRod G, Mega Water. S, and HyperStorm H to attack the group, but were interrupted by the arrival of the recently transformed Silver Man and his partner Blaze Woman-formerly Blaze the Cat-with the last Chaos Emerald.

Eggman's boasts that the Chaos Emeralds provided the real power, far outclassing the likes of Wily's Genesis Unit, marked a sour note n the relationship between the two scientists. After a brief argument as to which of them was better, they decided that it would be best determined by seeing whose nemesis survived the longest. With their welcoming party defeated, the doctors greeted the heroic intruders in person in company of the eight remaining Robot Masters: Knuckles Man, Shadow Man, Rose Woman, Silver Man, Blaze Woman, Charmy Man, Vector Man, and Espio Man. Watching as their minions battled the heroes, the doctors broke into a round of congratulating each other, and explained to the heroes their plan to pit them against the Roboticized Masters in a tournament. Proto Man refused to go along with it, and when he broke off to locate Dr. Light, Eggman surprised Wily by dispatching five of the Masters to pursue him. The pair returned to the Wily Egg, where they soon received the unpleasant news that Sonic and Mega Man had restored the trio of Masters pitted against them to normal.

However, Wily remained quite confident, reminding Eggman of their Robot Master army; when his partner announced his decision to send Shadow Man against the heroes, a brief bit of confusion led to inspiration. With both the Robot Master Shadow Man and the Roboticized Master Shadow Man on their way to confront Sonic and Mega Man's party, Eggman also withdrew Silver Man and Blaze Woman from the hunt for Proto Man, though Wily urged him not to worry and reminded him of their many resources. Eggman then suggested creating a new vehicle, the Egg-Wily Machine X, as a precaution, and questioned why Wily was so pleased; Wily responded that Mega Man's greatest asset, Dr. Light, was their prisoner. His pleasure was short-lived, as Orbot soon reported that both Shadow Men had been defeated, with one restored to normal and the other destroyed. After losing Silver Man and Blaze Woman to the heroes as well, Wily and Eggman ordered Knuckles Man and Rose Woman to attack them, with orders to self-destruct as necessary.

Seeing their plans in danger of being thwarted, Wily began planning his betrayal of Eggman and dreaming of how he would put the Wily Egg to use back on Earth, unaware that Eggman was entertaining similar thoughts. Their fears seemed to be well-founded, as Knuckles and Amy were subsequently returned to normal as well, adding to the heroes' growing support force. To make matters worse, Bass and Metal Sonic reported the discovery of saboteur Rouge the Bat, who had damaged the Wily Egg's engines and caused them to lose much of their built up Chaos Energy. Rouge was soon cornered, and her release of the Chaos Devil-yet another of Wily and Eggman's combined ideas-only resulted in her own capture. The doctors sent her for Roboticization into Rouge Woman, and had repairs completed on the Wily Egg. Despite the approach of the heroes, the two remained confident, as an entire army of Robot Masters served as the Wily Egg's first line of defense.

The doctors' army soon met the heroes-now joined by E-123 Omega-in battle, while aboard the Wily Egg Albert and Ivo enjoyed some fun at the expense of Dr. Light. Much to their embarrassment, their pet minions crashed into each other and did absolutely no harm to Thomas, who then attempted to convince the evil doctors to abandon their insane plans of universal domination. Unlike Eggman, Wily showed no interest in Light's inexplicable knowledge of their plans-passed to him by Rouge-and claimed that Thomas was simply jealous of him yet again, claiming to be in "complete control." Thomas responded with "Ra. Moon.", and went on to cite several other examples from their altered world of times when Wily had believed himself to be in control only to end up needing Mega Man to save him. Ruffled, Wily ignored his old friend's pleas, and left to observe the battle, which found him shouting out suggestions to his Robot Masters. To his surprise, Eggman left with Metal Sonic in toe, and attempted to remedy the problem of Dr. Light permanently-by throwing him out of the Wily Egg.

Upon Eggman's return, Wily accosted him furiously, outraged at his attempt to murder Dr. Light, whom Wily had only wished to humiliate. Their friendship broken, the pair dispatched Enker, Punk, and Ballade to deal with Sonic, Mega Man, Tails, and Rush after the heroes boarded the Wily Egg. Dispatching Metal Sonic, Bass, and Treble as well, they set off to complete the Egg-Wily Machine X, both of them convinced that their partner was no longer worth keeping around longer than necessary to complete the plan. The two worked to complete their vehicle-with Eggman complaining about working on it himself and Wily muttering discontent over the name-while Sonic and Mega Man continued to travel deeper into the Wily Egg. The heroes managed to defeat the Mega Man Killers despite Tails being injured and forced to leave with Rush, and were relieved of the task of fighting the Chaos Devil by the arrival of Mega Man's old ally Duo. A battle with Metal Sonic, Bass, and Treble proved difficult, but the heroes managed to triumph in large part do to the weapons Mega Man had acquired from the Roboticized Masters. Unfortunately, the weary heroes were then caught off guard and captured by the Egg-Wily Machine X.

Awakening inside the Wily Egg's main reactor, the two heroes were forced to deal with the gloating of Wily and Eggman, who regained a brief bit of their old rapport until remembering their feud. Wily and Eggman then explained the full scope of their plan: to use the power of all seven Chaos Emeralds to reshape their universes at a whim, making them veritable gods. Upon learning that their efforts had the potential to destroy both their worlds, Wily railed on Eggman yet again, but was then informed that the Super Genesis Wave all seven Emeralds were to produce would undo all the damage. However, the arrival of Thomas' eight fighting Robot Masters-whom Wily had previously stolen but apparently chosen not to claim as part of his army-allowed Thomas, Proto Man, Knuckles, and Rush to breach the reactor chamber and free the heroes. Proto Man and Knuckles went after the doctors, who fled to the safety of the Egg-Wily Machine X; once inside, Eggman warned Wily not to draw too much power from the Chaos Emeralds for fear of disrupting the Super Genesis Wave.

With Knuckles threatening to break into his cockpit, Wily attempted to activate his personal defense systems, only to find them inoperable. After Eggman tried to do the same, the two doctors realized that they had sabotaged each other. Working feverishly as the two red heroes pummeled their craft, the two managed to get it working again, and soon had it fully repaired and charged thanks to the power of the Chaos Emeralds. Fortunately, Knuckles and Blues' efforts gave Sonic and Mega Man time to prepare one last nasty surprise for Eggman and Wily: with the power of the Emeralds and Mega Man's Super Adapter, the pair had transformed into Super Mega Man and Super Sonic. Even as the Super Genesis Wave spread out from the reactor, a massive battle raged between the doctors and their hated foes, ending in Wily and Eggman's defeat. Watching as the heroes prepared to restore their worlds to normal, Wily briefly wondered if he would have any recollection of these events. Noting Eggman's furious refusal to accept these developments, Wily exhorted him to at least show some dignity in defeat. To his shock, Eggman instead took off in what was left of their vehicle's head, leading to dire consequences for his home world even as Wily's was restored to its previous state.

Breaking Point (continued)
Wily awoke to find himself back in the Lanfront Ruins. Possibly due to the Genesis Wave's reversal, he had completely forgotten about discovering the Chaos Emerald, his encounter and plan with Dr. Eggman, his brief visit to the future thanks to the Genesis Wave, and the future information that he had received. The only thing about the incident he was able to keep, was a violent urge to stomp on a carton of eggs, leftover from when the two evil doctors betrayed each other. Confused, Wily used a nearby computer to help refresh his memory on his previous plan with Ra Moon. He then questioned Ra Moon, only for the computer to announce that the time had come to execute its plan. Wily attempted to dominate, reminding Ra Moon that he had built an amplifier into it to increase its power, only for the computer to attack him and plug its cables into his mind, allowing it to show him its history. It explained that it had arrived on Earth in ancient times and attempted to bend mankind to its will, rejoicing as its adherents and opposers did battle. Not content with primitive warfare, it buried itself and the Lanfront Ruins in preparation for a time when humans would be advanced enough to make their destruction more enjoyable for Ra Moon. Satisfied that the time had arrived, Ra Moon drove Wily into hiding, and began spreading its EM field across the world. To its knowledge, only the Wily Masters it had recreated or brought into being remained immune to its power.

Blackout: The Curse of Ra Moon
Fortunately for Wily, he had personally modified Blues to be immune to Ra Moon's EM Field, meaning that Break Man was not dependent upon Ra Moon's protection or susceptible to its control. Before returning to Wily, he further upset Ra Moon's plans by providing Dr. Light with information on a protective coating that could be used to reactivate Robot Masters affected by the field. Arriving at the Temple of the Moon, Break Man was attacked by Ra Moon-who recognized that it had no power over him-and was reunited with Wily, whom he quickly accosted over the situation. Retorting that Ra Moon's plans went far beyond what he had intended, Wily prevented Break Man from either confronting the computer himself or contacting the other Robot Masters, as he had no idea whether or not they would still be loyal to him. He then revealed his plan: to have Break Man protect him while he used the knowledge gained from examining Ra Moon to construct Ra Thor, a Robot Master intended to destroy the alien construct.

Break Man left briefly and returned with food, also reporting that a party led by Mega Man had arrived near the ruins and confronted some of Wily's first set of Robot Masters. Upon hearing Break Man's report that they appeared to still be loyal to him, Wily had Break Man leave to investigate further. A strange alliance soon resulted, with Break Man and Wily's original eight Robot Masters teaming up with Mega Man's team to battle the second set of Wily Masters, all of whom were under Ra Moon's control. Wily soon intervened in the battle, ordering the completed Ra Thor to destroy Ra Moon, only to have Ra Moon take control of it due to it being based on the same technology. Desperately, Wily turned to Mega Man as his last hope, while Ra Moon announces its intentions to use Wily's technology against him as he intended to do against it with Ra Thor.

Tiring of the fight, Ra Moon removed the first line of Wily Masters' immunity to the EM field, only for Mega Man to destroy Ra Thor using what remained of the Special Weapon power he had previously absorbed. Undeterred, Ra Moon fulfilled its promise by creating a new minion based on the Yellow Devil: the Ra Devil. Despite the monster's power, Wily found a glimmer of hope when Mega Man shot it in the eye and failed to do any damage. Realizing that Ra Moon had to be protecting its new guardian with its own power, Wily reasoned that Ra Moon itself would be vulnerable if they acted quickly. To his astonishment, Mega Man converted both of his arms into Mega Busters, the act of firing which would overload his systems. After making a final request of Wily-to return his body to Dr. Light-Mega Man fired, destroying Ra Moon. Without it, the EM field fell, Wily's Robot Masters returned to normal, and the Ra Devil melted away. Surprisingly, Wily kept his promise and returned to Light Labs with Guts Man, Bomb Man, Cut Man, Rush, and the badly damaged Mega Man.

Redemption
Unbeknownst to the Light Robot Masters-who had all been knocked out during the battle with Ra Moon-Wily was less than thrilled after Mega Man's sacrifice, as yet another of his plans had been thwarted. Furthermore, Shadow Man had departed upon viewing the broken form of his master, Ra Moon. However, Wily soon saw new opportunity, and ordered his Robot Masters to depart, with Break Man joining and leading the seven new Masters on a hunt for Shadow Man while the others set to work on a new Wily Castle. He then performed minor repairs on the Light Masters-enough to get them working again-and was confronted by Guts Man and accused of trying to tamper with his systems again. Fortunately for Wily, Cut Man and Bomb Man talked him down, and the group then set off to get Mega Man back to Light Labs. In order to keep Mega Man's Integrated circuit from failing, Wily was forced to reroute much of his power, a fact he was quick to inform Auto of during the repair effort on Mega Man.

Once Mega Man was stabilized, Wily noted with his usual disgust that Thomas credited Mega Man with all the heroism of saving the world, when it was Wily who saved Mega Man  and'  Blues. The remark earned Thomas' ire, and he demanded to know how Albert had been involved in the events surrounding the EM field and Mega Man's current condition, as well as what had happened to Blues. Responding on the last subject, Wily honestly reported finding Blues and repairing him before seeing him leave to attack Mega Man (leaving out his role in provoking Blues to that action). Roll questioned why Blues would attack and then provide the formula for the anti-EM coating, and Auto then asked why they hadn't contacted the police to have Wily arrested. Wily exploded, again reminding them that he had helped save Mega Man, and was calmed down by Dr. Light, who suggested that he take a chance to clean himself up until the time came for his story to be heard. Several days later, Mega Man appeared to be on the mend, but Wily was arrested by Agent Roslyn Krantz and her partner Gilbert D. Stern. Outraged, Wily accused Light of betraying him, and was then informed that the agents had refrained from arresting him sooner at Light's request, primarily due to all that Mega Man had done.

Not content to accept this generosity, Wily called the group out on their duplicity, noting that they were willing to bend the law because of Mega Man but were willing to take him into custody when he claimed that Ra Moon forced him to serve it. To his surprise, Mega Man took that moment to awaken, and volunteered to travel to the Lanfront Ruins and find proof of Wily's innocence. Light also informed Wily of his intent to argue hard for leniency, hoping that the sentence against Wily would be reduced to house arrest and that Light would be able to pay his bail. Outside, several reporters waited to question Wily, who put on a show of being a victim forced to act against his fellow humans and hoping to be vindicated. While Wily spent time in jail, Mega Man and several others-Thomas, Roll, Dr. Pedro Astil, Plant Man, Dr. Cossack, and Pharaoh Man-traveled to the Lanfront Ruins to learn the truth. Despite Cossack's beliefs that Wily was withholding the truth from them, the evidence they found did more to support than refute any of Wily's claims.

Wily soon found himself in court, and continued to play up his story of being a victim of Ra Moon's control, though he was willing to admit to having previously done evil of his own accord. In the end, it was decided that Wily had no role in the attacks by Break Man and the other Robot Masters, but that his violation of both the bans against his work on robotics and the United Nations quarantine of the Lanfront Ruins had earned him five years of house arrest. This sentence was to be served with Thomas Light as Wily's guarantor, meaning that Wily would be living at Light Labs with his old partner. The two scientists soon got to work on a new project, the Dynamic Operations Circuit Robot, which had the ability to utilize several Robot Master systems at once. While Wily claimed that it was a more efficient tactic than building several Robot Masters, Mega Man saw its potential as a weapon even more powerful than Mega Man, which was Wily's true plan for the robot.

Thomas broke up the tension of the situation and demonstrated his continued trust in Albert by showing him his newest project: Gamma, a massive robot designed to handle crises like Ra Moon. Amazed by Light's good faith in him, Wily couldn't help but admire his old colleague; unfortunately, their conversation was then interrupted as Light was frozen in time by Flash Man. Having penetrated Light Labs using Break Man's old entry codes-unchanged since he had left the lab as Blues-Flash Man reported that Wily's latest castle was nearly complete and that Shadow Man had joined their forces, bringing Wily's total number of Robot Masters to seventeen. Conflicted between his desire for world domination and the kindness shown to him by Thomas, Wily had Flash Man leave. Some days later, he attended the unveiling of Gamma at Titanium Park, and upon complaining that he was no good at public speaking was reminded by Roll that he had done just fine when threatening the denizens of Mega City. As Light commenced the ceremony, Wily felt his old jealousy returning, and contacted his Robot Masters to proceed as planned rather than calling them off as he had briefly contemplated. To his surprise, Thomas then called him up to the podium, and the pair went on to discuss the evolution of robots and the role Gamma would fill.

In the midst of proceedings, Wily's second set of Robot Masters-Shadow Man included-arrived to steal Gamma's Energy Elements, the power source for the massive robot. Light recognized their designs as ones that he and Albert had created together, and Wily responded that Ra Moon had stolen them. Attempting to keep up pretenses, he stopped Mega Man from attacking them, and made a show of trying to reason with them. After the Robot Masters made their getaway, Wily broke down in false sobs, proclaiming that he had ruined his one chance at redemption. Noticing Plum and other reporters taking note of his words, he enjoyed a smirk at his apparent success in convincing them of his good intentions.

Dawn of X
After being questioned regarding where the renegade Robot Masters might be hiding out, Wily came up with a possibility: the lab where he had built the Wily Walker prior to being sanctioned for his work on robotics. Mega Man, Pharaoh Man, and Bright Man-the latter two sent by Dr. Cossack, who had joined the hunt-traveled to this laboratory, hidden beneath a mesa, and found that-despite Wily's "sincere" assurances-several of the defenses were still active. Questioned by Dr. Light on the matter, Wily restated his conviction that this lab was the most likely destination for the Robot Masters, since all of his other old facilities had been seized by the government while this one was deemed too dangerous to dismantle. His suggestion that Ra Moon might have programmed it as a fall back location for the Robot Masters did little to shake Dr. Cossack's mistrust in him, and Wily secretly hoped that his old facility would prove to be the end of Mega Man. Thanked for his help by Dr. Light, Cossack took the opportunity for a jab: "Cossack-built Robot Masters--helping Mega Man clean up Dr. Wily's messes in 20XX." Feigning amusement, Wily questioned how Kalinka was doing now that the Ra Moon crisis was resolved, and a shaken Cossack retorted that she was no longer scared since there were no more monsters or "mad scientists."

The trio of Robot Masters eventually came across the Wily Walker, and Wily revealed that his decision to equip it with chemical weapons was the reason for his robotics ban, enraging Dr. Cossack. Wily claimed that he intended to replace them with different weapons prior to being taken into federal custody, and transmitted the deactivation code to Mega Man. In reality, the code he sent served to activate the Wily Walker, though he blamed the "mistake" on Dr. Cossack distracting him. The activated Wily Walker proves more than a match for the three Robot Masters, and Mega Man is seemingly crushed after acting to save Bright Man, although he survived. Wily then pretended to help Mega Man, but was secretly scheming that Mega Man be defeated, also realizing that he has taken everything into account so that even if Mega Man won against the Wily Walker, he'd still have to contend with both all eight of the third generation Robot Masters and Doc Robot, also pretending to call the other Robot Masters for help. He also came up with the idea to modify Bright Man's shining ability into a Special Weapon to take out the Wily Machine, to Dr. Cossack's reluctance.

Legends of the Blue Bomber
Afterwards, Wily observed Mega Man's heading off to space to confront the eight Robot Masters based on a tip from agents Stern and Krantz. Although he wished Mega Man luck, he secretly realized his robo-goose chase will at best end in a close call, meaning either Mega Man dies or he gets the Energy Elements for his master plan. After Top Man was defeated by Mega Man, he attempts to retrieve Top Man's IC chip and the Energy Element, although because Mega Man feared that the portable transporter would scramble the chip to be glitched or worse, Wily had to settle for the Energy Element for the time being. In addition, he also experienced a slight hitch in his plan after Roll had Gamma locked down, with Dr. Light agreeing largely because of Wily's ban on robotics and his just barely getting the Judge's good graces from the trial earlier, thus forcing Wily to store them for later, as well as shooting a dirty look at Roll afterwards.

He also sent messages to the Robot Masters, giving Roll some suspicions and prompting her to have Auto investigate. Wily also sent Break Man to retrieve the second generation's weapons data and IC chips (presumably for the finishing touches of Doc Robot), although while most of the Robot Masters reluctantly surrendered their belongings without a fight, Quick Man fought Break Man, forcing Wily to contact Quick Man directly to order him to do so. To stall, he also forgot to flush the toilet when Auto checked up on him. Ultimately, Mega Man managed to defeat the four Robot Masters on the Mining Asteroids, giving him some panic, and eventually having him warn Magnet Man about Mega Man's arrival. He was ultimately found out by Auto, although Wily managed to rip out vital components in Auto's systems under the guise of fixing his audio systems to silence him when he confronts him.

This action ultimately resulted in a lockdown of the lab being activated by Dr. Light shortly thereafter, due to Roll discovering Auto's disassembled body. Wily, after the lab was locked down, deduced Roll's discovery and report to Dr. Light, and lamented that he couldn't complete the Doc Robot now, only for Break Man to enter the room to ask for a report from Wily (due to Break Man, original name Blues, possessing security bypass codes in the event that he wished to return home when he ran away earlier). He then managed to complete Doc Robot, burst out, and then confronted Dr. Light and Roll at the command center with Break Man and the now-fully operational Doc Robot, simply taunting Dr. Light's shocked question of why he was doing this by stating he was the best, and fully intended for Dr. Light to learn this.

The Ultimate Betrayal/Prisoners of War
Dr. Wily continues to try and pressure Dr. Light to let him into Gamma's hangar, also telling Doc Robot that neither fanning flames nor blowing more stuff up will be necessary so long as Dr. Light cooperates when asked. When Dr. Light warns him that Mega Man is going to be returning to stop Wily, Wily, after acknowledging that Mega Man is the other son of Dr. Light's who barely managed to defeat the eight Robot Masters, revealed that he anticipated that outcome and made sure Break Man was positioned to deal with him, also informing Dr. Light that Break Man, aka Blues, is his son now. He also dodged a swing from Roll's broom, resulting in it breaking off against Doc Robot. After two attacks from Doc Robot, Dr. Wily tells Doc Robot to be careful with the "splash damage", with Doc Robot (who was composed of the IC chips of all eight Wily Robot Masters) protesting that it's hard to process due to Wily shoving them all in Doc Robot's chassis. Wily then mentioned that Doc Robot's current actions was a glitch due to this, and also inferred that he'll have Doc Robot murder Roll and Dr. Light with a random attack if Dr. Light doesn't cooperate, with Dr. Light reluctantly caving to Dr. Wily's demands. As Dr. Light proceeded to grant access to Gamma's hangar to Wily, Wily begins to taunt Dr. Light, eventually pushing Light beyond his limits and causing the latter to violently grab Wily before Doc Robot interfered. Using the teleport systems for the Energy Elements, Wily proceeded to teleport Gamma and himself out while taunting Dr. Light, also ordering Doc Robot to completely obliterate the upper lab, intending for Dr. Light to suffer as he watched his legacy crumble. Wily then contacted Break Man and told him to return to his castle, also admitting that Roll and Dr. Light are still alive in Gamma's hangar. Unknown to Wily, however, Break Man leaked the codes to Wily's Castle to Mega Man, as he wanted to fight his brother at full capacity.

Later, he is working on a device to allow him to control Gamma directly (as Gamma had a voice-activation protocol in the event that it was stolen). He was later gloating about his genius and estimated that he only had a few more hours before he achieves full synchronization with Gamma, provided there weren't any interruptions. As if on cue, Doc Robot arrived and alerted Wily about Mega Man's arrival, to Wily's shock and confusion, as no one knew about the location of the island, let alone the castle, before learning that Break Man most likely leaked the codes. He then proceeded to observe the battle with Mega Man, and was so entertained by the battle that he even admitted that he considered forgiving Break Man for leaking the codes to his enemy in the first place, although he also remembered that Dr. Light sent backup the last time Mega Man and him fought, and prepared for the Castle's defenses to be scrambled in the event of a break in, and also had Doc Robot deployed in the event that Mega Man got far enough. Ultimately, Wily managed to complete the control unit and attached it to Gamma just after Mega Man disabled the gargantuan robot's automative control unit.

Upon reactivating Gamma, Wily then pursues Rush and Mega Man, and proceeds to taunt the Blue Bomber of inheriting Dr. Light's naivety, as well as boast that Mega Man, regardless of his "minor victories", can't stand against the power of Gamma. Mega Man then scolds Wily, stating Gamma was meant to support Dr. Light's dream to help people. Wily then mentions that it "is" going to help people by gloating about himself and his plans. However, Mega Man deduces that the only way to stop Gamma is to remove the Energy Elements, with Gamma being destroyed soon thereafter, with Wily even being believed to have died as a result. In actuality, he survived, albeit with a concussion and a fractured arm and leg, and was recovered by a group belonging to a mysterious individual known only as Mr. X.

Wily later awoke in one of Mr. X's facilities, where Mr. X himself greeted the doctor and informed him that he now worked for him and the X Foundation. Much to his surprise, Wily was then provided with new resources to allow him to make another takeover attempt, part of Mr. X's plan to make the world see the evil of robotics. Just as Wily was beginning his new operations, a Genesis Portal opened-an event that Mr. X had expected-and Sigma emerged to pull Wily through into another world.

Worlds Unite
Wily found himself dragged through to the world of his old ally Dr. Eggman, who had similarly been press-ganged into Sigma's service. Since Wily had previously forgotten about his first team-up with Eggman, the evil doctor from Sonic's world, who had managed to get out of the situation with his memories of the encounter intact, had to refresh his memory about the whole thing. However, upon recognizing that Wily no longer remembered their previous feud, Eggman convinced him that they had previous been turned against each other by Dr. Light. Menaced by Sigma and his Deadly Six allies, the pair were forced to work on converting Eggman's facilities into a new base for Sigma. However, Eggman convinced Wily that they could defeat Sigma and their respective nemeses together. After converting Eggman's facilities into a Mechaniloid manufacturing plant, the pair fitted the Deadly Six with armor that was later used by Sigma to control them. They also began work on Sigma's Unity Engines, but also suggested that he recruit Mega Man and Sonic as minions. After the pair were captured by the Deadly Six, Wily and Eggman set about turning the pair into Sigma's newest pawns, Sonic Man and M'egga Man.

After succeeding in their task, the malevolent doctors watched eagerly as their creations attacked Mobotropolis and Mega City. Wily noted that he had adapted Quick Man's processor for use in Sonic Man, and complimented Eggman's genius in combining his Egg robot designs with Mega Man. The pair then watched eagerly as Sonic Man engaged the Light Robot Masters, and proved to be more than a match for them. They then joined Sigma in watching the ensuing battles between the newest Roboticized Masters and the Freedom Fighters, several of Wily's Robot Masters who had been restored by Dr. Light, Knuckles, Break Man, Quake Woman, and Gemerl. The defenders proved unsuccessful, and the corrupted heroes succeeded in setting up two of Sigma's Unity Engines. As the two worlds began to merge together, their power was fed into Sigma's Master Engine, which in turn fed it into Sigma. This realization terrified Wily, though Eggman tried to assuage his worries by reminding him of their contingency plan: secondary programming in their enslaved nemeses that would cause M'egga Man and Sonic Man to attack and cure each other. Their plan was to set the two heroes and their allies on Sigma; unfortunately, the arranged battle took place off of the Lost Hex. The pair were thus forced to retreat, only to find themselves pursued by three of the members of the Deadly Six.

As they were hiding from their hunters, the pair were unexpectedly greeted by an unlikely-and in Wily's eyes unwelcome-ally: Xander Payne, an anti-robotics terrorist. While Wily was convinced that Xander had only his demise in mind, Xander surprised the pair by opening a Genesis Portal and leading them through it. They wound up on the Sky Patrol, the Freedom Fighters' mobile base and the temporary residence of all the allied heroes. After being briefly astonished by Wily's survival, Mega Man joined the others in placing the three intruders in the brig, where Wily and Eggman admitted to having turned them into Roboticized Masters but blamed the idea on Sigma. They then informed them of the Maverick leader's whereabouts on the Lost Hex, but would only agree to provide information if they were freed from the cell. The pair were then given access to the technology aboard the Sky Patrol, and while watching Tails work on the various robots Wily noted that Zero of the Maverick Hunters looked like something he would build. He also learned that Shadow Man had only joined the Wily Numbers allied with Dr. Light in preparation for a future betrayal, which Wily advised him to hold back on until later. He and Eggman then set to work on a weapon to aid in the battle against Sigma while the heroes engaged Sigma's waiting army of Mechaniloids.

Wily and Eggman continued working with Sally Acorn urging them on, and eventually had their Egg-Wily Uppity Robot Scrambler Cannon operational. Just in time, they employed it against the Maverick Hunters, Gemerl, and the Robot Masters, who had turned against their comrades by the Deadly Six's abilities. The weapon overheated immediately after firing its first shot, but succeeded in freeing the robots and destroying the mind control armor on the Zeti. Unfortunately, Sigma soon revealed his massive new body and his latest minions: an army of time-cloned Mavericks. Before Eggman and Wily could get their weapon working again, it was destroyed by Tornado Tonion, and Wily found himself being carried to safety by Mega Man of all beings. When questioned, the hero responded that he had failed to save Wily during their last meeting and wanted to make up for it. Wily accused him of simply acting according to the Laws of Robotics, but Mega Man asserted that it was something he wanted to do. Most of the Mavericks soon dispersed to other worlds while a handful remained behind to finish off the weary heroes, but a group of allies from the world of Street Fighter soon arrived to aid them. While the heroes prepared to disperse to other worlds and Eggman contacted Metal Sonic to bring his Chaos Emerald to be united with those of the Freedom Fighters, Wily and Eggman schemed as to how they could get to the Master Engine. The answer, once again, proved to be Xander Payne, who escorted the doctors through a Genesis Portal.

The trio found the Master Engine while the heroes faced Sigma in a final battle, and managed to cut off his connection to the Master Engine. However, Sigma's actions had already left reality dangerously unstable, but the doctors believed they could correct it using the Master Engine's power and recreate reality in their own image. However, Xander forced the pair to move away from the device, and used some of its power to open one of his Genesis Portals to the moment in Sigma's time right before he had traveled back to the present. Wily and Eggman tried to warn him of the potential consequences of altering history, but Xander felt it worth the risk and destroyed Sigma's virus form, preventing his trip back in time. The events of his attempt to conquer the multiverse were thus reversed, leaving Wily back in Mr. X's facility. This time, he was able to keep some memories of his involvement in the aborted timelines, Wily realized that Mr. X was an older Xander Payne, who had been sent back a few decades into the past due to the alterations, and swore revenge. He also was determined that if he and Eggman ever met again, they would achieve victory over their nemeses.

Red Shift
As part of his continued schemes, Wily soon contacted Break Man, who like Mega Man and his allies believed Wily to be deceased due to Xander's actions undoing their cross-dimensional encounter.

Short Circuits
Wily appears in many of the series' humorous "Short Circuits" strips, starting in Issue 2 where he has Cut Man perform a number of humiliating tasks before dispatching him to battle Mega Man. He also appears in Issue 4's strip where he is imprisoned after being defeated by Mega Man, and disagrees with Mega Man's assessment that their experience has been "a great first adventure" due to his defeat. Issue 6 finds a sleeping Wily being awakened by Time Man acting as an alarm clock, only for the ringing Robot Master to be knocked out by "Snooze Man", aka Guts Man. Issue 10's strip features Wily, having completed his new set of Robot Masters, putting their abilities to use in relaxing before embarking on his next scheme.

In Issue 11 Wily deals with the problems caused by Crash Man-such as crashing his vehicles and computer-but then has the ingenious idea of sending him in to the stock exchange. Issue 12 finds Wily receiving Mega Man's surrender after revealing his new allies: the aliens from the classic arcade game Space Invaders. Issue 13's Short Circuits doesn't feature Wily himself, but rather a mockup created by Auto for his reenactments of Mega Man's adventures. Issue 16 finds Wily heading to the Advanced Robotics Trade Show in disregard of his Super Adventure Rockman subplot at the time of the "Spiritus Ex Machina" arc. However, he and Reggae then turn around after witnessing the explosion of the Emerald Spears' bombs.

Issue 17 features the first of a series of "Failed Robot Masters", with Wily creating-and being disappointed by-Origami Man. Further failure ensued in Issue 20, where Wily's Police Man chose to berate the scientist over his criminal activities instead of infiltrating the police force as intended. During "Worlds Collide", Wily appeared not only in "Short Circuits" but in the "Off Panel" strips of the Sonic series. His first appearance was in Mega Man Issue 24, where he and Dr. Eggman were granted a reprieve from taking on their united foes by a crossover rule stating that the heroes had to battle each other first.

Sonic Universe Issue 51 featured Wily in the Off Panel, modifying Bass with bio-data from Sonic and greatly altering his appearance. Sonic the Hedgehog Issue 248 saw Eggman replace Metal Sonic's engine with a Mega Buster, with Wily expressing doubts about the idea that proved well-founded. Mega Man Issue 25's strip also featured Wily, claiming that neither the battle between Mega Man and Sonic nor their fight with Wily and Eggman were the greatest battles of the crossover: that honor went to a struggle between pirates (Pirate Man and Captain Whisker) and ninja (Shadow Man and Espio the Chameleon). A crayon drawing of Wily appeared in Mega Man Issue 26, where he and Eggman were apparently upset over the new friendship between Bass and E-123 Omega.

Sonic Universe Issue 53 found Wily expressing concern to Eggman over the absence of Tikal, who had appeared when they captured Chaos to create the Chaos Devil. Eggman assuaged his concerns by informing him that Tikal was a pacifist; unbeknownst to both of them, the Echidna girl was holding a pep talk with the Yellow Devil in an effort to get it to abandon violence. Mega Man Issue 27 featured another failed Eggman and Wily team concept: the Roboticized Master Big Man, who proved incapable of anything but fishing. With the crossover ended, Wily returned in Mega Man Issue 35's strip, where Mega Man complained about having him as a nemesis only to be introduced to Sigma by Mega Man X.

In Issue 35, Wily is mentioned by Mega Man while complaining to X about Wily being the worst villain ever, resulting in X offering to trade him for his own archnemesis, Sigma, causing Mega Man to take it back when seeing Sigma. Issue 36 found Wily recounting a heroic-and utterly false-tale of his efforts to stop Ra Moon while wielding a sword similar to that used by Sword Man, only to be enslaved by the villainous computer. Issue 40 had Wily, alongside Sigma, bursting through the panel, just as X was to explain to Mega Man what his future will be like. He was also mentioned by Needle Man in Issue 43's Short-Circuits as being the inventor of Sudoku. Issue 44's strip saw Wily introduce his latest creation, Dubstep Man, only for him to be destroyed by Bass.

In Issue 45, Dr. Wily and Dr. Light are holding a symposium on biology with everyone fleeing, with their discussing what the Robot Master Guts Man (depicted as the internal anatomy of the human body) would look like, with implied failure.

Other references to Dr. Wily in Sonic the Hedgehog

 * Just as Dr. Wily referenced Dr. Eggman in Mega Man #23, Eggman referenced Wily as Albert in Sonic the Hedgehog #247 (portions reprinted in Free Comic Book Day 2013) as he prepared to depart into the Skull Egg Zone.
 * Dr. Eggman refers to Wily as Albert again in Sonic the Hedgehog #252 as he blames his former partner for their failure.

Trivia

 * This interpretation of Dr. Wily introduces a number of new elements to the character, including a history of being banned from work with robotics.