Mega Man (original series)

Mega Man classic refers to the original series of Mega Man games. The first game, Mega Man, was introduced on December 17, 1987 on the Famicom and Nintendo Entertainment System (NES). Most of the main games in the series are referred to as "Mega Man" (or "Rockman" in Japan) followed by a number (2, 3, etc.). However, the ninth game in the classic series (not counting the "side-stories") is called Rockman & Forte, or Mega Man & Bass. The tenth official game in the classic series is titled Mega Man 9, which has a retro look, having the 8-bit appearance of the NES Mega Man games.

The basic story of the game revolves around the robot engineer Dr. Thomas Light, his robotic "children," Rock (a lab-assistant) and Roll (a housekeeper), and their struggle against Dr. Albert W. Wily. As the series began in 1987, Capcom set it in the early-21st century. The first four games (as well as some of the side-stories) take place in the ambiguous years of 200X (sometime between 2000 and 2009). However, Mega Man 5 and beyond set a more ambiguous date of 20XX (presumably 2010 or later, although it could be anytime between 2000 and 2099).

Below is a basic time-line of the events of the Mega Man Classic series (including most major games):

Official Timeline
Below you will find the official timeline of the classic Mega Man series. This is simply a listing of what period these games take place and in what order:


 * Mega Man (December 200X, listed as 20XX in Mega Man: Powered Up)
 * Mega Man 2 (200X,six months later)
 * Mega Man: Dr. Wily's Revenge (200X, soon after the events of Mega Man 2)
 * Mega Man (PC) (200X, before Mega Man 3)
 * Mega Man 3 (PC) (200X, after PC1 but before Mega Man 3)
 * Mega Man 3 (200X, a few months after Mega Man 2?)
 * Mega Man 4 (The game takes place in 20XX, but the intro mentions the events of the previous games as taking place in 200X)
 * Wily and Right's RockBoard: That's Paradise (Sometime after Mega Man 4)
 * Mega Man: The Wily Wars (After Mega Man 3 and Mega Man 4, since Dr. Wily was presumed dead after Mega Man 3 and did not want to risk revealing his plans for involving Dr. Cossack)
 * Mega Man II (20XX, after the events of Mega Man 4)
 * Mega Man III (20XX, a few months after Mega Man II)
 * Mega Man 5 (First game to directly reference 20XX in the opening sequence)
 * Mega Man (Game Gear) (After Mega Man 5)
 * Mega Man's Soccer (After Mega Man 5 as Beat is present)
 * Mega Man IV
 * Super Adventure Rockman (Sometime after the events of Mega Man 5, but could be before Mega Man IV or after Mega Man V)
 * Mega Man V
 * Mega Man 6
 * Mega Man 7
 * Mega Man: The Power Battle (Sometime shortly after Mega Man 7, as characters from that game are present)
 * Mega Man 8
 * Mega Man 2: The Power Fighters (Sometime shortly after Mega Man 8, as Duo is present)
 * Mega Man: Battle and Chase (Sometime after Mega Man 8 and Mega Man 2: The Power Fighters, as Duo is present.)
 * Mega Man & Bass (Japanese instruction manual says Dr. Wily is 57 years old)
 * Rockman Gold Empire (Sometime after Mega Man 8 and Mega Man & Bass)
 * Rockman and Forte: Challenger From the Future (After Mega Man & Bass)
 * Rockman Strategy (After Challenger From the Future)
 * Mega Man 9 (MM9 apology scenes are seen in the ending, from previous games and Mega Man & Bass)

Actual timeline
This is a timeline created based on the basic timeline shown by official sources.

Ancient times

 * ca. 20,000-19,000 B.C. : Ra Moon comes to Earth (Some sources list this date as 19,7XX B.C.)
 * Humanity is both blessed and cursed by Ra Moon with knowledge and hated to cause war and destroy themselves.
 * After an unknown time, Ra Moon seals itself away.

Notes: The exact year of the arrival and sealing of Ra Moon is unknown, but it is known that it arrived very early in the development of Earth, most likely in what historians would call pre-history (thousands of years ago). The estimates here have been provided to provide a sense of the time during which the events most likely took place.

Unknown dates

 * Sunstar/Sungod is sealed away.
 * The Intergalactic Police Force (which Duo is member) is formed.
 * Mega Man fights "the Genesis Unit" from Mega Man: The Wily Wars; this was definitely after MM3, but most likely after MM4 as Wily did not want to reveal that he was alive and plotting against Dr. Cossack.
 * Wily and Right's RockBoard: That's Paradise
 * Mega Man's Soccer
 * Mega Man: Battle & Chase

20th Century



 * 1958: Thomas Light and Albert W. Wily are born.


 * ca. 1970: Mikhail Sergeyevich Cossack is born (he seems to be in his early-40s by the events of Mega Man 4).


 * 1986: Thomas Light and Albert W. Wily receive PhDs, in Robotic Engineering, Thomas Light graduated highest in their class, while Wily was second. (they would be 28 years old).


 * ca. 1995: Dr. Light found Light Labs to use computer and electronic technology to benefit mankind. Dr. Wily is his assistant in English sources, while he is his rival in Japanese sources.


 * 1998: Mikhail Sergeyevich Cossack receives his PhD from Vruer University, most likely in Electrical or Computer Engineering.

21st Century



 * 2000s: Light Labs begins research and development in the field of robotics and simple artificial intelligence, developing beneficial robots, such as the Mettaur construction robot and the Sniper Joe police units.


 * ca. 2002: Kalinka Cossack is born (she is around 9 years old by the events of Mega Man 4).


 * 2005: With advances in research in artificial technology and robotics, Proto Man is created based on the design of the Sniper Joe, but with a far more advanced AI and advanced weapons system. However, before Light Labs could finish testing him, Proto Man's sense of independence led him to go AWOL.


 * 2006: Light and Wily decide to create a pair of robots with the "failure" of Proto Man, and thus, Rock and Roll are created. They believe that the two of them will be happy together and provide a mutual support that will overcome any sense of independence.  Rock was to serve as a lab assistant while Roll would be a housekeeper.  Then, the team went on to construct what became known as the Industrial Series:  Cut Man, Guts Man, Ice Man, Bomb Man, Fire Man, and Elec Man (with Time Man and Oil Man being added in Mega Man Powered Up).


 * 2007: Dr. Light wins the Nobel Prize in Physics for his creation of the Robot Masters. Additionally, he wins the LIT Manual Design Contest, which his partner Dr. Wily participated in and only won a runner-up status in.


 * 2008 : (Mega Man) Out of jealousy for Dr. Light, who won the Nobel Prize and the Manual Design Contest the previous year, Dr. Wily "revolts" by reprogramming all of the Industrial Robots in the lab (failing to reprogram Rock and Roll, but considering them just a "lab assistant and housekeeper"), and then fleeing to his new fortress (in a city called "Monstropolis" in English sources). Knowing that the armies of the world won't be ready to stand against Wily's new robot legions, Rock volunteers to be converted into a fighting robot, who soon becomes known as Mega Man.  Mega Man defeats the Robot Masters (who are eventually reprogrammed by Dr. Light) and overcomes Dr. Wily, bringing him to justice (or so he thought).




 * 2009: (Mega Man 2:The Enigma of Dr. Wily) Six months after his defeat, Dr. Wily builds eight brand-new Robot Masters (all of his own design) and leads a second attack on the world. Once again, Mega Man is called into action, and he manages to successfully defeat Wily and crush his army of robots for a second time.


 * (Mega Man: Dr. Wily's Revenge) Dr. Wily revives eight of the Robot Masters from his previous two assaults as well led by a brand-new robot known as Enker (the first of the Rockman Killers), but Mega Man had already faced these foes before and, as such, Wily fell again.


 * (Mega Man 3:The Death of Wily?!) A few months have passed since Wily's past uprisings and Dr. Wily is trusted by Dr. Light once again and works at Light Labs. The two endeavor to create a peacekeeping robot known as Gamma, but the energy crystals required to power Gamma are found on mining planets that are protected by powerful Robot Masters.  Mega Man is called upon to retrieve these crystals, but Light gives him the newly-created Rush, the "robo-dog."  In the end, Wily steals Gamma upon the return of the crystals and announces that he was behind the Robot Masters.  Mega Man goes after him and ultimately defeats him and, upon his defeat, his skull castle is destroyed and it seems that he dies in its explosion/collapse.  The AWOL Proto Man also makes an appearance, seemingly helping Wily (but some have interpreted him as helping Mega Man by "training him").


 * 2010 : (Mega Man 4:A New Ambition!!) (Mega Man 4 is the first game to take place in the year 20XX, although the game's story references 200X as the year Rock was created. The game takes place a few years after that).  A year after the Gamma Incident, the world had been living in peace and thought that Wily was gone for good.  However, Dr. Light received a letter from a mysterious Russian scientist named Dr. Cossack, claiming to be the greatest scientific genius in the world and having been far too long overlooked, challenging Light and Mega Man to a "contest" of sorts.  Cossack's new army of Robot Masters began to make their move, so Mega Man, with his newly equipped Mega Buster went after Cossack.  In the end, it turned out that Cossack's daughter Kalinka had been kidnapped by Wily (who was very much alive and, it appears, hiding in Russia), but luckily Proto Man "betrays" Wily and rescues her.  Mega Man heads to Wily's citadel and defeats him once more.




 * (Mega Man II) Dr. Wily breaks into the Chronos Institute and steals the Time Skimmer, traveling 37.426 years into the future (to the year 2047). Wily kidnaps Mega Man, reprograms him, and names the new robot Quint.  Upon his return to his present time, Wily builds another army of robots led by previous Robot Masters and Quint, but Mega Man manages to defeat them and Quint (and ultimately Wily).


 * While Wily is visiting the future (the year 2047), he first experiments with the technology available during that year. He first creates a robot known as Rockman Shadow (R-Shadow for short), but he discards this prototype, finding him unusable.  He later turns his attention on reprogramming the real Mega Man.


 * (Mega Man III) Dr. Wily has been making a bid at control of the world's oceans, and with an army composed of previous Robot Masters led by a new Rockman Killer named Punk. Mega Man, having already encountered these foes, once again manages to overcome them and counters Wily's ambitions.


 * (Mega Man 5:Blues' Trap!?) About two months later, Proto Man went to Light Labs and kidnapped Dr. Light, leaving behind his signature yellow scarf. Then, an all-new army of Robot Masters under his command began to attack the cities and the Space Port near Light Labs, so Dr. Cossack, who had become Light's new colleague at Light Labs, armed Mega Man with the new robotic bird, Beat, and sent him after Proto Man.  However, when he confronted him, the real Proto Man showed up and revealed the fake to be a robot called Dark Man, and upon its defeat, Dr. Wily showed up and challenged Mega Man to come and get Dr. Light.  Mega Man defeated Wily and freed Light, but when Wily's castle collapsed, Proto Man had to save them from being crushed by the building.




 * (Mega Man IV) A new army, led by the Rockman Killer known as Ballade makes its attack, but once again Mega Man foils Wily's plot and destroys the revived Robot Masters.


 * (Super Adventure Rockman) A powerful energy signal is detected in the Amazon, and Dr. Wily goes to investigate. In the ruins of an ancient temple, Wily comes upon an ancient supercomputer that calls itself Ra Moon.  Ra Moon has the power of shutting down robots and other electronic devices (sort of like a virus), and thus United Nations attempts to stop Dr. Wily prove futile.  Roll is one of the robots affected, and as such, Light sends Mega Man to the Amazon to put a stop to Wily's plans.  Fortunately, Mega Man gets help from the Industrial Robot Masters (from Mega Man), who provide useful tips and give him items as he progresses.  He encounters various Robot Masters from Mega Man 2 and Mega Man 3, and once he makes it into the temple he finds that Wily is powerless to stop Ra Moon.  Ra Moon transforms into a powerful fighting machine, but with Wily's help, Mega Man upgrades and can perform a Double Rock Buster attack that manages to defeat the supercomputer, thus putting a stop to his "virus."


 * (Mega Man V) 3 months later (near the end of 2010), a mysterious band of robots from outer space, known as the Stardroids, come to make a bid for domination of the Earth. Rock and Roll were pleasantly walking through a field when Terra, the leader of these robots, attacked and quickly defeated him.  Thus, when he awoke in Light Labs, Light informed him that his Mega Buster was not strong enough to defeat these extraterrestrial visitors.  Light then gives him an upgrade known as the Super Arm and a robotic feline called Tango.  However, upon the defeat of the Star Droids, Mega Man discovers that they were really created by Dr. Wily, but their technology was indeed from outer space.  Wily had discovered an ancient "alien" robot known as SunGod and had used his design to construct the Star Droids.  However, when Wily woke up SunGod, he refused to obey Wily and attacked him.  However, he did intend to battle Mega Man since Mega Man was a powerful robot and, in the end, Mega Man proves victorious.


 * 2011 : (Mega Man 6:Greatest Historical Battle!!) One year later, peace had finally begun to settle over the world. To celebrate the new era, the mysterious billionaire Mr. X held the First Annual Robot Tournament, inviting the greatest engineers from all around the world to show off and compete with their greatest creations.  Mr. X was the founder of the X Foundation and the Robot Union, a force designed to counter the evil desires of Dr. Wily.  However, at the final round of the tournament, Mr. X revealed that he had reprogrammed the final eight contestant robots and was going to use them to lead his new army of robots to make a bid for world domination.  Mega Man was called into action yet again, but this time he had the ability to combine with Rush to form Jet Mega Man and Power Mega Man.  When he defeated Mr. X, he found that Dr. Wily had simply been impersonating the real Mr. X (who had most likely been kidnapped).  Thus, Mega Man had to chase Wily down to his new skull compound and defeat him, but once he did, he managed to bring him into the authorities, who tried Wily and had him imprisoned...




 * 2012 : (Mega Man 7:Confrontation of Destiny!) Six months after Dr. Wily's imprisonment, four robots that had been hidden away in his lab activated and broke him out of prison and began to wreak havoc in the city. Mega Man went to investigate and, upon his arrival, met up with the mysterious Bass and Treble, a robot and his dog who appeared to be after Wily as well.  After defeating the four Robot Masters, Mega Man returned to Light Labs, only to find that Wily attacked the Robot Master Museum and stole Guts Man.  Then, four more Robot Masters attacked.  In the attack, Bass was damaged (by Shade Man), so Mega Man sent him to Dr. Light for repairs. However, when he returned to the lab, the lab was badly damaged, and Dr. Wily appeared on the screen to mock them and announce that Bass and Treble were his creation.  Mega Man set out for Wily's lab to get his revenge.  In the end, he defeated Bass and Treble and crushed Wily, then saying he should put an end to Wily and stop the suffering he causes. Wily stated his programming, which adhered to Asimov's "laws of robotics", prohibits harming humans, but Mega Man said he is more than a robot.  Bass interfered in time to save Wily, and they managed to escape...


 * (Mega Man: The Power Battle) Mega Man, Proto Man, and Bass take on Robot Masters from Mega Man through Mega Man 7 and, in the end, take down Dr. Wily, each with their own motives.


 * 2013: (Mega Man 8: Metal Heroes) Two powerful robots battle each other in outer space and, in the process, damage each other and go careening to Earth. They land on an island that is occupied by Dr. Wily and, as such, Wily harnesses one of them and uses its extraterrestrial powers to make a new batch of Robot Masters.  Mega Man, who was battling Bass in the city, is summoned by Roll (really by Dr. Light) to go to the island to investigate.  He finds Dr. Wily salvaging the robot and, in the process, discovers the second robot in a crater and sends it to Light Labs to be repaired.  Mega Man defeats the four Robot Masters that attack various places on the globe and, when he returns to Light's Lab, he finds that the robot is undergoing repairs.  Then, while talking to Light, the robot breaks free and heads out into the desert.  Mega Man follows him, fights him briefly, and then Proto Man intervenes and tells him that Wily's new fortress, "Wily Tower," is up ahead.  Mega Man goes ahead and is captured by Wily, but the robot saves him and introduces himself as Duo (a member of the Intergalactic Police Force ).  Duo explains that the other robot contained "Evil Energy" within it and that Wily was using that energy to make his robots more powerful.  Mega Man needed to defeat the other four to open the entrance to Wily Tower.  He did so and managed to defeat Bass and Treble and, in the end, Dr. Wily.  Mega Man was injured in the process, but Duo saved him and left him out in the desert, where Proto Man was there when he awoke and told him that Duo said "Thank you..."


 * 2015 : (Mega Man & Bass) In the Japanese Rockman & Forte manual, Dr. Wily is noted to be 57 years old. A couple years have passed since Duo's visit to Earth, and a robot calling himself the robot King appeared and began to recruit other robots to form a new Robot Army.  He believed that robots were not meant to simply serve humans, but rather that they were superior and therefore should be the "masters of the Earth."  Dr. Wily was ousted from his own newly completed skull compound and sought refuge at Light Labs and, as a result, Bass was sent alongside Mega Man to put a stop to King's rebellion.  When King attacked the Robot Master Museum, Proto Man attempted to stop him, but King cut him in half with his axe and Mega Man and Bass sent him to the lab and confronted him.  King withdrew, claiming not to have time for them, and left them to his subordinates.  Once his army of Robot Masters was defeated and the "Hatches" that locked his fortress were unlocked, the two made their way through his fortress and confronted him.  None of their attacks appeared to phase him, so the newly repaired Proto Man came again, charged up his Big Bang Attack (even though it would severely damage his internal systems), and destroyed King's shield.  Mega Man and Bass managed to defeat King and, upon his defeat, Dr. Wily appeared on the screen and asked King what was wrong with his "brain washing."  He remotely repaired King and then King fled to another room and combined two previous war machines into a giant battle machine, but was defeated again and begged the two to stop Wily's ambitions.  Mega Man and Bass then went to Wily's floor of the castle and put a stop to the madness.  In the end, Mega Man was sad that an innocent robot was destroyed, but then he received a letter from King and found out that everything was alright.  Bass, however, was mad that Dr. Wily had plotted against him, but Wily claimed he wanted to find out if King was stronger than he was.  Proto Man teleported in, saw plans for a "King II" on Wily's computer, and then destroyed it, leaving the two to quarrel amongst themselves...


 * (Mega Man 2: The Power Fighters) Mega Man, Proto Man, Bass, and Duo return to take on more of Wily's robots (from Mega Man through Mega Man 7) to achieve various goals and for their own reasons and, in the end, Wily is once again defeated. Dr. Wily reveals to Bass that he is working on a robot superior to him and silhouette of Zero is displayed on one of Wily's monitors (only seen on Bass's lone ending).




 * 2016 : (Rockman and Forte: Challenger From the Future) Humans and robots live together in harmony in Symphony City.  However, R-Shadow and the Dimensions come from the year 2052 and begin to attack the city's citizens in order to draw out Mega Man.  Mega Man, who had been once again battling his nemesis Bass, had to put aside his differences to investigate this new enemy: Who was R-Shadow and why did he look exactly like him?  Wily sent Bass to go and fight the Dimensions because they were attacking the region near his new fortress.  R-Shadow claimed to be Quint, the robot designed by Dr. Wily six years ago.  Was he there for revenge?  When Mega Man and Bass defeated the Dimensions and brought R-Shadow down, he revealed the truth: he was actually a prototype of Quint.  Dr. Wily had experimented with future technology during his visit to the future and first designed R-Shadow, but then discarded him in favor of his project to reprogram Mega Man.  Although R-Shadow seemed to "die," Dr. Light managed to repair him and reprogram him, thus making him a member of the Light Labs team.


 * (Rockman Strategy) A few months after the events of Rockman and Forte: Challenger From the Future, a group of high-tech space invaders known as the Constellation Droids arrive at Dr. Wily's lab and, under the threat of death, force him to cooperate with them.  Not long thereafter, plants all around the world begin to die.  Moreover, earthquakes and other devastating events begin to rock the planet.  As newscasts are broadcast around the world alerting the populace to these problems, Dr. Wily takes control of the airways announcing his newest plot for world domination.  However, Dr. Light and Mega Man have no idea that Apollo and Luna, the leader of the Constellation Droids, are the masterminds of the plot.  After building up an army to fight the Droids, consisting of Duo, Eddie, Auto, the rescued Proto Man, Fan, and many others, Mega Man takes down the Droids one by one and confronts Apollo and Luna.  He discovers that they came to Earth when they discovered that the planet was slowly dying, believing that mankind was the primary reason for the planet's slow death.  Yet, after a long discussion with Dr. Light, it is ascertained that the virus destroying plant life was created by Dr. Wily, who engineered it in order to lure the Droids to Earth in the hope that they would set out on a mission to "purify" the planet.  In the end, the Droids assist Mega Man and friends in their effort to bring the evil scientist to justice and then go back to whence they came...


 * September 18, 2016 : Dr. Light completes the capsule of Mega Man X, realizing that his work on X would not be completed within his lifetime (he was nearing 60 years of age). Light knew that X was a "new breed" of robot which possessed the ability to make his own decisions, and this ability brought with it serious implications.  X could be both a blessing and a danger- he did not have to follow Asimov's "laws of robotics." Thus, during his construction of X, when X asked him why he called him X, he answered that "X is a variable of unlimited potential."


 * 2017: (Mega Man 9: Ambition's Revival!!) About a year has passed since the events of Rockman Strategy. Just when people thought peace would once again exist, robots all over the world began going crazy!  It soon became apparent that these robots were those created by Dr. Light!  As phone calls came pouring in to Light Labs, Dr. Wily interrupted all television programs to announce that these robotic riots were not his doing.  He then continued to show video evidence that proved Dr. Light's involvement in the recent violent outbreaks.  To make matters worse, Wily gave the account number to his personal bank account and announced that he would accept donations to build his own robot army to counter that of Light.  Mega Man quickly volunteered to clear Light's name and was sent out to investigate the source of the problem...Before long, the police came to Light Labs to arrest the good doctor, but Light went along quietly to prove his innocence.  Meanwhile, Mega Man went after the Robot Masters and, after he defeated a few of them, discovered that they were scheduled to be decommissioned and sent to the junkyard because they had reached the expiration date assigned to them by the government.  Once the final Robot Master had been taken down, Mega Man brought back one of the robot's internal memory units to Auto for investigation.  As it turned out, Dr. Wily had convinced the robots, who were scheduled for demolition, to rise up against their human masters rather than be destroyed.  All the robots wanted to do was have a purpose, and they certainly did not want to be sent to the scrap heap!  After they had viewed the video, Dr. Wily burst into their lab and stole the memory circuit and then withdrew to his newly constructed Skull Castle!  Mega Man had to make his way through the fortress, fighting powerful robots built with the money Wily received from donations from those concerned with the robot uprisings.  In the end, Mega Man defeated Wily once again, and showed him footage of nine defeats he had dealt Wily (MM1 - MM8 and "Megaman & Bass").  Although Wily seemed contrite and apologetic, he tricked Mega Man into thinking that Dr. Light was, in fact, imprisoned in a jail cell in the next room.  Although Proto Man warned him that it was a trap, Mega Man went to investigate the cell and was electrocuted and Wily's lab self-destructed.  Thankfully, Proto Man returned and teleported Mega Man out of the lab just in time.  In the end, Light was released from prison and then found useful purposes for all of the Robot Masters he had designed but which had reached their expiration dates.


 * ca. 2040 : Dr. Thomas Light and Albert W. Wily die, most likely of "old age" (they would have been 82 years old).


 * 2047 : Dr. Wily visits this year by using the Time Skimmer. At first he experiments with the technology of the mid-21st century, designing the prototype which he calls R-Shadow.  However, he later discards R-Shadow in favor of his project to kidnap and reprogram Mega Man into Quint.


 * 2052 : R-Shadow creates an army of futuristic robots known as the Dimensions and travels back to the year 2016 with the intention of confronting and destroying Mega Man.


 * ca. 2055 : Dr. Mikhail Sergeyevich Cossack dies, most likely of "old age" (he would have been 85).

Unknown Information and Theorized Events

 * It has never been directly stated whether the transition from 200X to 20XX was meant to show a transition in time or to provide for more ambiguity. However, events that have been retconned to 20XX (such as Mega Man: Powered Up) can still take place in the 200X time period, as 20XX simply means somewhere between 2000 and 2099.
 * It is unknown exactly when Mega Man X is sealed by Dr. Light as the only date given is September 18, 20XX. X was initially meant to be sealed for 30 years, but ended up being sealed away for a century.  He ended up being unsealed by Dr. Cain a couple years after the year 2114 (he was discovered on April 14, 2116). Therefore, the year 2016 fits ideally with this date.
 * Although it is unknown whether X and Mega Man ever met, or if Mega Man was ever aware that Dr. Light was designing X, there is no reason why this could not have been possible as Bass was aware of Dr. Wily's building of Zero. Note there is an episode in the megaman cartoon that involves X traveling back in time and meeting megaman.
 * Capcom has as of yet not said what happens to the characters between the Classic and X series, but in an interview with Ryan Scott of 1Up.com, Capcom's Hironobu Takeshita said that the idea of Zero activating and fighting and/or killing Mega Man and company "seems like a rumor that goes around in certain circles, but it is not official. Certainly, the two series are set in different time periods, but they share the same spectacular world. There might be a bridge for the chronological gap someday, but I don't think it's time yet."
 * Perhaps Mega Man, Rush, and company, after the end of the Wily Wars, are deactivated and sent to the Robot Masters Museum. Proto Man, most likely, succumbs to the lethal breakdown of his nuclear reactor (as theorized in this Mechanical Maniacs article), unless, of course, he finally goes to Dr. Light for repairs.
 * As for what happens to Drs. Cossack, Light, and Wily? They could die of old age, or perhaps of something else.  For now, one just has to theorize.  Still, we know that they are present in some form or other in later series' (as A.I., etc.).  Perhaps one day Capcom will go into more detail as to how that comes about.