It is kinda dumb, but I personally believe it mostly transferred to Sigma during the X4 flashback battle, while whatever was left of zeros original programming laid dormant until X5.

@aranryan-9440 my thought process was Zero when he was freed was crazy already, Wily couldn't control him so he put him in stasis, while working on the virus, when he was freed, the virus got out, infected an injured Sigma after it was able to infect and distract Zero. That infection caused him to turn good and in 5's bad ending, Sigma, who has now transcended his body and seems to have made connections to Wily, infects Zero, but to wake up his dormant programming, that is, to kill X. That's why uninfected Zero is a laughing, raving lunatic while Awakened Zero seems more collected and calm. He has his infected so his personality is calmer, but Zero being an advanced robot, not a reploid, he is still bound by his programming.

@@Lucidplays34 I mostly agree, but the virus and zeros evil canceling out is just stupid. However, maybe the virus cause whoever infected to deviate from their original programming, like Sigma becoming a dangerous Maverick leader when he was the strongest Maverick Hunter.

@aranryan-9440 Sigma is a reploid. He has free will. Zero predates reploids. It stands to reason he does not. That was the premise for the longest time. Mavrick = criminal reploid. Not infected. It's why 8's ending pisses me off so much that it completely forgets the premise of the series, that reploids have free will and can just choose to be evil.

Its children of bodom - trashed lost and strungout

REAL