User blog comment:The Crazy Terror/PE Proposal: Dr. Wily/@comment-37233793-20190916232751/@comment-442429-20190917225502

Eh, no, it's pretty explicit that he left all those vaccine pills behind on purpose.

And even if the virus effected the events of the X series, there is Zero evidence that it was intentional. The official Complete Works books state clearly that he created the virus to "purify Zero's body", because he wanted Zero under control, not going berserk killing people indiscriminately. This is evidenced on the bad ending route in X5, where Zero's awakened form just calmly challenges X, meanibg this is what Wily had always intended him to be.