Wily really is behind the plot
The whole thing started because Shock Man hit Justice Man with an electrical attack and damaged his mental matrix irreparably. It's pretty abnormal in the Mega Man series for a regular attack to do that sort of damage... unless the attacker is infected by the Maverick/Zero virus. My guess is that Shock Man was infected by one of Wily's prototypes for the virus as a test subject, and through him the infection spread to the others. It likely wasn't yet strong enough to make them go outright berserk, but it was enough to cause robots that were unhappy with their current positions to react violently. This would explain why the robot masters reacted as they did rather than taking less violent routes. Also, since it seems to be a surprise in the X series when a Maverick is resurrected this may explain why their voices were "silenced forever". If they went Maverick, it may be that they can't be brought back the way other masters have been.- Jossed: It turns out that Shock Man's attack on Justice Man did not damage his mental matrix, it was his independent thought that did.
- Why not split the difference?: That while Shock Man's attack would still have been the proximate cause of Justice Man's malfunction, his irregular mental matrixnote led to the worse-than-normal damage that he suffered. And, in effect, the game itself. The post-game autopsy would be instrumental in the development of X's suffering circuit. This also would not require Wily's involvement (Zero virus or not) though it would keep the cause of Shock Man's original malfunction Mysterious.
