Dr. Weil

Dr. Weil, or Dr. Vile (Dr.バイル) in the Japanese versions, is a fictional villain from the Mega Man Zero series series. He is not related to Vava/Vile from the Mega Man X series and, contrary to fan speculation, there is no direct evidence that he is Dr. Wily from earlier games. It should be noted that "Weil" is technically a correct translation of Bairu, if assumed it follows German phonetics; however, "Vile" is the name acknowledged by official Japanese media, proven by the fact that the boss logo in Mega Man Zero 4, which is no longer an Omega symbol, is the letter V in the Japanese game (it is changed into W in the English releases).

Between Mega Man X and Mega Man Zero
Dr. Weil, who was born at an unknown date during or before the Maverick Wars, was a human scientist who participated in the project to design the original Cyber-Elf, the Mother Elf. In this project, Dr. Weil was a coworker and rival of the ancestress of the future resistance leader Ciel, and both of them had significantly different views on how the Maverick Wars should be resolved. Weil made weapons to use against the Mavericks and specialized in Reploid revival, while his partner worked on analyzing the viral energies within Zero's original body (which had been salvaged after he entered a period of stasis) in hopes of finding a cure for the Maverick Virus. Although the Mother Elf was completed and was successfully used by X to end the Maverick Wars and eliminate the virus altogether, Dr. Weil was dissatisfied with these results. He believed that the reploids should pay for the carnage their wars caused and should submit to humanity. Weil eventually took control of the Mother Elf and reprogrammed her, transforming her into the Dark Elf, thus triggering the horrifying Elf Wars.

Additionally, seeing as how the body's original consciousness had been removed, Dr. Weil successfully used his retained genius to steal and fully repair Zero's original body and give it a new identity, Omega. With the Dark Elf to control Earth's Reploids and Omega to destroy any and all who opposed him, Weil nearly destroyed the entire planet.

By the time X and Zero (now in a new copy body built by an unknown party) were able to end the war, it had decimated 90% of all reploids and 60% of humans in its flames. Omega was eventually disabled by X and Zero, and his remains were sealed and launched into orbit.

Meanwhile, for his crimes back on Earth, Weil was sentenced to be contained within a biomechanical suit that would prevent him from deterioration and death. He was then exiled to the wastelands he had made, never to age or die, but only suffer eternally therein. Having been exiled, Dr. Weil began to plot his revenge on humans and reploid alike.

Mega Man Zero 2
Dr. Weil is first mentioned in the ending sequence of Mega Man Zero 2 as the man who placed a curse on the Mother Elf, thus turning her into the Dark Elf. He can also be heard (but not seen) talking to Omega after the credits.

Mega Man Zero 3
Weil makes his reappearance from his imposed exile at the end of the game's opening stage, with a supposedly resurrected Copy X.

Near the end of the Maverick Wars, Weil used the Dark Elf and copies of her, the Baby Elves, to seize control of the Reploids. He also constructed the devilish Reploid known as Omega, whom was defeated by X and Zero with a Final Strike and exiled into space as punishment.

In the game, Copy X makes Weil the Leader of the Neo Arcadian Army. He leads the search for the Dark Elf and the Baby Elves and eventually combines Omega with the Dark Elf. Weil eventually kills Copy X with a booby trap on his body that detonates when he attempts to access his Seraph form.

With Copy X dead, Dr. Weil invokes Ordinance #8 and becomes Leader of Neo Arcadia by unanimous vote. He then uses Neo Arcadia's resources as he sees fit, to gain control of Reploids through the combined powers of the Dark Elf and Omega, in order to punish the citizens of Neo Arcadia for his banishment.

Though Zero destroys Omega in the end of the game, Weil remains Ruler of Neo Arcadia.

Mega Man Zero 4
The fourth game in the series begins with the premise of Weil as absolute ruler of Neo Arcadia. Under his rule, humans and Reploids are equally oppressed, with all those that oppose him labelled as Mavericks. His reign of terror became so unbearable that in Mega Man Zero 4, a group of humans escaped to Area Zero, where the remains of the Eurasia space colony not only crashed, but also helped revive vegetation.

Seeing Area Zero as a threat, Weil devises Operation Ragnarok to obliterate it, thus forcing people to live in Neo Arcadia. The plan involved distracting the Resistance with half-hearted attempts to destroy the ecology in Area Zero, whilst he completed the Ragnarok Satellite and its huge Energy Cannon. He was prevented from firing it by Craft, who ended up firing it at Dr. Weil himself, destroying Neo Arcadia and killing many civilians.

Unfortunately, Dr. Weil survives and teleports into Ragnarok. He attributes his survival to his regenerative armor, which the humans of the time put him in before his exile. Weil states that it can heal all wounds faster than normal, prevents him from aging, and prevented him from dying. Additionally, to ensure that he would never forget his crimes, the humans also turned his memories into data and preserved them within this apparently partially metallic and partially carbonic body.

In the end he decides to crash Ragnarok into Area Zero, and when Zero confronts him, he merges with the Ragnarok Core in order to defeat the Reploid.

However, after defeating him once, Weil comes back. Eventually, Zero decides to destroy the Core, destroying Ragnarok, Weil, and (presumably) himself along with it.

Mega Man ZX
It is possible that Dr. Weil returned as the major evil of Mega Man ZX, in the form of the Biometal Model W (Model V in the Japanese version). Model W is the original Biometal, formed from the pieces of Ragnarok, which Dr. Weil fused with, that fell to Earth at the end of Mega Man Zero 4. Sometime after the end of Mega Man Zero 4, the original commander of the Guardians (Ciel) analyzed data collected from Model W and learned that Model W has the ability to drive both Machines and Humans to madness. In response, she built the six Biometals (those used in the game) to stop Model W.

A decade prior to Mega Man ZX, the small fragment that Ciel studied was stolen by Serpent. The power of Model W led Serpent to create various Maverick out-breaks, and, in turn, form Slither Inc. to stop the Mavericks, which caused many Cyber Elves to be released from the deaths of the victims. These Cyber Elves are then captured and used to "awaken" Model W at the end of the game.

In Aile's story, Prometheus and Pandora, two major antagonists, state that Serpent, the hero, themselves and even Model W are but pawns to " the man who created Model W", Master Albert, whom made his appearance in Mega Man ZX Advent as one of the Sage Trinity and the creator of Model W and Model A.

It could also be that like the other BioMetals, who retained their own conciousness they had as Reploids, Weil is still concious at the time, but prefers not to speak and instead decided to manipulate possible targets in order to continue his goal of forming a utopia under his role, using his manipulated subject to give orders.

Personality
"...Though my body appears thus... I am still human...!"

Weil generally displays a calm, manipulative nature, but underneath that he's clearly psychotic. By re-building Copy X he gained power in Neo Arcadia, and later set the stage for a battle between Copy X and Zero, which he made sure Zero would win. This shows Weil's intelligent side. Also, when he sent Omega in the missile to intercept the Dark Elf, he counted on the Baby Elfs to fight Zero as a distraction for not fighting Omega, meaning he knew Zero would go on the missile. He showed his psychotic side when he commented of how much he enjoyed controlling all Reploids with the Dark Elf. Another symptom of his psychotic persona is that in Weil's desire to destroy Area Zero, he wants to bear witness first-hand to the crashing of Ragnarok into Area Zero by staying on the station during its crash. He firmly thinks that, thanks to his regenerative armor, he can survive the crash, regardless of what happens to his "human side".

Despite his manipulative nature, Weil's most significant weakness is his knack to underestimate his enemies, especially Zero. He thinks that Zero has no chance of defeating Omega, especially when the latter surfaces in his most powerful form. Also, after Zero defeats Craft for the second time, Weil fired a "warning shot", indicating that Ragnarok was still operational. This alerted the Resistance to the imminent threat of Ragnarok's crashing into Area Zero, and the warning shot was like a challenge to his enemies to try to stop the crash.

Weil shows a constant hatred of Reploids, as well as humans for exiling him. He also seems to have, ironically enough, some sort of pathological hatred towards intellectualism in general, due to his saying "Risou Dato... ZAREGETTO DA!!!", which roughly translates to "Ideals and stuff... IS UTTER NONSENSE!!!", or "Ideals?! WHAT A LIE!!", before his fight with Zero.

Trivia

 * As much as Dr. Wily is to the original Mega Man, and Sigma to Mega Man X, Dr. Weil could also be perceived as Zero's own personal archenemy.
 * Chikao Ohtsuka is also the Japanese voice of the villain Dr. Eggman in the Sonic series.
 * Weil gives a similar battle start line to Omega: He says "Ware ga akuma da!", which loosely translates to "I am an evil demon!" or "I am the devil!", which is similar to Omega saying "Ware wa Meshia nare!", which loosely translates to "I am the messiah".
 * He resembles the "Star Fox" villain Andross. He even has a similar backstory to him. Both were once world renowned and respected scientists, then fell from grace from a lust of power, instigated a crime that resulted in them being banished from their home country/home planet.
 * In addition, his role mirrors that of another villain, Emperor Palpatine/Darth Sidious. Both were leaders of a military role and used cunning manipulation to earn a desirable result that would end them up with immense power, no matter what the cost, at the same time, casting the heroes off as the true villains in the process, only to have their believers suffer oppression. In addition, both characters had a messiah under their wing, with Palpatine having Darth Vader and Weil having Omega in hopes that if they died, then their 'creations' would carry out their wills in their place (Interestingly, both of them were 'corrupt' versions of existing heroes [Or in the case of Omega, the corrupted body of said hero], though both were ultimately created by evil figures). In addition, both arranged for the creation of a horrific battle station used to destroy large populations to terrorize his empire so they wouldn't rebel from his rule.
 * Even though Weil is not featured officially until the 3rd game, he is responsible for many of the events in the first two. His corruption of the Mother Elf led to X's original body being used to seal away the Dark Elf, which in turn led to the creation of Copy X, having serious repercussions in the first two games.
 * Three different designs - young, middle-aged, and elder - were proposed for Weil's character. The final design of Weil was based on the latter character concept.
 * Canonically, Weil is the only Mega Man villain who has successfully destroyed the world, leaving it in a post-apocalyptic era.
 * Although he has no official connection to Dr. Wily, the two Doctors have other similarities besides the structure of their names: they both continued to menace the world long after the demise of their mortal bodies (Dr. Wily during Mega Man X with the Maverick Virus, and Dr. Weil before and during Mega Man Zero as a cyborg, and during Mega Man ZX as the original Biometal).
 * There is a slight reference to the 1998 movie Armageddon prior to Zero's final battle against him. Right after Zero sees the Ragnarok core, Dr. Weil says "Hehehe! Welcome to your front row seat to the end of the world!!". One of the main characters (and arguably the main antagonist), Rockhound, says something similar when watching the meteor they are trying to destroy get closer to Earth.
 * Dr. Weil mentions that humans enjoy ultimate power and having everything obey your every command. Sigma mentions a similar description of humanity to General when telling him to get Repliforce to fight against Humanity/the Maverick Hunters.
 * By the way the mysterious voice in Megaman ZX Advent's speaks, like "I will select a new host for Model W." or "I will wait for my work to be discovered.", one may imply that the speaker is no one else more than the true Model W: the one that retains Dr. Weil's personality data and memory like X,Zero,and the Big Four had.