Dr. Wily Has Been An Evil Villain Consultant (With Different Aliases) In Megaman X?

Megaman X as an obvious direct sequel to Megaman (classic) does have some stuff left to the imagination of the players. Granted, it's been at least 100 years since the original series ended and much can happen. Did Dr. Wily find a way to cheat death only to find out that he wasn't really having much of a choice? Dr. Wily didn't want to take the position lower than the Big Bad. However, it seems that he was left without a choice. There are theories that two characters namely Serges and Isoc are both robotic forms of Dr. Wily. It's also said that Dr. Wily is somehow a stream of consciousness that travels from one body to another. So, how does this work? One of the episodes of the third season of Transformers hast he once-mighty Cobra Commander after several years since COBRA was defeated. There's no more COBRA organization - only Cobra Commander going by the name of the Old Snake. The only way Cobra Commander could survive in the episode "Only Human" was to...