Maverick Virus
The X Series revolves around the Maverick Virus, which is a confusing concept to most Mega Man X fans. This article will try and break down the concept and the history of the virus.
What it is
The Virus is the driving force behind the Mavericks. It was first directly referenced in MMX3 and Dr. Doppler believed he had found a cure for the virus. (He had actually only made a placebo.) The Virus removes all inhibitions within a Reploid or Mechaniloid and urges them to destroy whatever they can.
Furthermore, the virus evolved when it came into contact with Sigma... see below.
Origins
The original ideas for the virus was as follows: Zero was the original carrier of the virus. (See MMX4 and a variety of Japanese Sourcebooks) At some point when Sigma and Zero fought before MMX, Sigma became infected. It may have been originally developed by Dr. Wily, possibly a manifestation of Evil Energy.
(It should be noted that Zero was seemingly purged of the virus. We know that Dr. Cain examines him (MMX4) but it isn't expressly stated that he removes it. It is possible that Zero was implanted with the 'Suffering Circuit', see below for more details.)
Sigma
With Sigma, the virus grew and evolved with his personality. Sigma was created by Dr. Cain as the perfect Reploid. He had the most advanced DNA computing systems and more. As the leader of the Maverick Hunters, he had access to the most advanced Reploid army of the time. The Virus does not appear Sentient until it reaches Sigma. It should be clearly stated that the virus evolved WITH Sigma: essentially, anymore, Sigma IS the Virus. It is believed through somebody infected, Sigma can control them, or at least, manifest his will in them.
Sigma has been able to be restored at least 8 times due to the Virus. In MMX8 it is believed he was killed once and for all, but in MMZ+ it's revealed the virus did in fact last some time longer, making Sigma last longer.
Elf Wars
During the Elf Wars, an ancestor Ciel, (a scientist of sorts) developed the Elf Program. This program was able to eradicate the Virus, or so it seems.
Suffering Circuit and True Origins
In a source book titled Rockman Zero Complete Works, the virus's origins are explained. X was built with a Suffering Circuit, a program that gave him his calm attitude and ill-will towards violence. This was developed by Dr. Light.
When Dr. Cain made Reploids/Repliroids, he copied the Suffering Circuit and implanted it in the new reploids. Unfortunately, there was a design flaw and in some reploids and mechaniloids, this caused them to be violent.
As Dr. Cain examined Zero, he implanted the Suffering Circuit into him, trying to make him normal. It worked, to an extent. Zero had a program designed to make him a homicidal maniac.
The murderous program was transferred from Zero and into Sigma when they fought. Sigma had the Suffering Circuit, but because of his Reploid defect, the the circuit didn't do its job and the homicidal personality came into play. Here the two components of Zero and X became a true virus as it mixed with Sigma.
When these two programs 'crossed streams' the suffering circuit became a Virus, making one have inhibitions to the opposite of the Suffering Circuit. Basically, with the virus, you were the opposite of X. You wanted to kill and hated the ideas of peace and benevolence.
With Sigma, the Virus had a 'perfect' reploid. With the X and Zero programs, and Sigma's, the Virus was born, causing the Maverick Wars that lasted countless years.
MMX1-4
In the first four games, Sigma's virus spreads and infects other reploids, making them Mavericks, and more importantly, HIS mavericks. The virus was found by Dr. Doppler in MMX3.
MMX5
During the events of the Eurasia incident, it is revealed that a mercenary named Dynamo released a virus into the colony, (the Colony Virus) that would cause the colony to crash into earth. The Sigma Virus and the Colony Virus mixed to form the Zero Virus. This Virus 'purified' Zero, making him stronger. (Most likely by having more of the 'Homicidal' program he was meant to have, it overrides the Suffering Circuit, allowing him to kill without regret.)
MMX6
The Zero Virus eventually became the Nightmare Virus. Originally not meant to become canon.
MMX7 on up...
Humans tried once again to enter space so they needed copy-reploids. Axl was made as the prototype. After him, all Copy-Reploids were made with a complex DNA pattern mixed with all the DNA's of the strongest Reploids from the past, including Sigma. These reploids cannot become infected, at least so it is claimed. But, since their internal DNA has Sigma in it, perhaps they are already infected.
Does the Virus cause all Mavericks?
It is worthwhile to note that the Virus doesn't cause all reploids to be mavericks. In other words, reploids CAN go Maverick. In MMX8 Lumine says some can go maverick at will which means simply that a reploid can CHOOSE to be a Maverick by attacking humans and other reploids. Lumine believes that Sigma isn't the source of being a Maverick.
Other reploids, such as Storm Eagle, chose to be Maverick, partly because their computing drives them to it. Vile/Vava has a defect, making him a maverick. It isn't clear if this is the common Suffering Circuit problem that existed before the maverick virus outbreak.
Differences between Sigma Virus and Maverick Virus
The Sigma Virus defines the virus that is directly related by Sigma, and potentially, the virus that Sigma uses to directly control those infected. The Maverick Virus seems to not be so evolved, and very active in just turning a reploid maverick, not necessarily being controlled by Sigma.
Final Notes
There are many theories floating around about how the Sigma Virus has overall infected the Mega Man series.
It may have been present since the classic series as Evil Energy. Zero was created with Bassium, an energy not to be confused with Evil energy, but may have been infused with it. (Although it does not appear so, Duo was on earth to eradicate all traces of Evil Energy and then left at the end of, or soon after MM8. In Rockman and Forte, Dr. Wily doesn't seem to be using Evil Energy and King was stated to be a prototype for a new version of robots. It isn't all that long after this that he creates Zero. So Zero's program may or may not be directly linked to Evil Energy. (EE doesn't appear in the X series yet.)
Some believe that the 'reaverbots' of the Mega Man Legends series are mechaniloids that are infected by the virus. The 'Reaver Eye' (giant red eye) is seen in Mega Man Zero, and some link it to the third eye of Sigma. This would explain their irrational aggression to 'diggers'. They may also be defensive simply because they are programmed to protect the ruins.
Dr. Weil/Vile is a cyborg and may have contacted the virus, making him even more evil. His Model W/V bio-metal turns those around it evil. The bio-metal is infused with Weil's soul. It may or may not have a connection with the Virus.
As of MMZ, the virus is believed to have been crushed, although 'Mavericks' are still frequent.
Also, Zero believed his original body had something to do with the virus, which it did. To try and eradicate the Virus, he basically seals away his old body which surfaces later as Omega.
Sources
Mega Man X (every game including Maverick Hunter X was used to write this article. The Japanese Sourcebook: Rockman Zero Complete Works was also used.