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Background Pony #5CC8
In the end the only one who knows the truth is Keiji Inafune, someone should ask him.
Aurora Moon
Economist -

@Cyborg_pony  
Model W can resurrect and revive the consciousnesses of those absorbed into it. Its possible Wily/Albert did this ahead of time to clone his mind, and the copy was dormant in Master Thomas until the original’s death. With the right tech, this copy could have undergone constant update to keep memories between copy and original matching up until the original’s death. Given precisely how long Wily would have lived by this point, it’s entirely possible such tech could exist. Especially with the blurring of the line between humans and reploids. You’re forgetting just how much time Wily would have had to set in place numerous back-up plans, and develop the technology needed to fuel them.
Aurora Moon
Economist -

@Zennistrad  
Then there’s ZX Advent, with one of the 3 leaders of Legion, who’s first name is Albert, and I’m pretty sure his last name is Wily. And considering what he did in ZX/ZXA using Ragnarok and Weil’s consciousness from MMZ4(Model W, basically), its pretty obvious he probably set shit up in MMZ3 and 4 to happen that way through manipulation of Weil back before the Elf Wars.
 
So Wily didn’t just survive into the X series, but all the way thru Zero and into ZX/ZXA as well, where he became the true villain as a whole once again. Let’s not forget the fact that the Mega Men in ZX and ZXA were all secretly infused with Master Albert’s DNA, which as long as Wily would have lived by now..he could have easily developed such technology. Weil could have even been his first test subject on this!
Captain L

@Zennistrad  
I’ve heard the theory that Isoc was Wily. There’s also evidence of Serges playing the same role. It’s hard to claim anything when neither of them got much time (seriously, Isoc played no damn role in that game).
 
The truth of the matter is, in the Japanese version of X6, Zero outright says he has no idea how he’s still alive. Which fits with him asking Dr. Light. Blame the terrible translation.
Zennistrad
Bronze Bit -
The End wasn't The End - Found a new home after the great exodus of 2012

@Captain L
 
You want to know what I think actually happened there? I think Zero lied, because he didn’t know who repaired him.
 
And do you want to know who I think that was? Doctor Wily. No, really, there are plenty of hints in the Mega Man X series that Doctor Wily is somehow still alive, possibly as a reploid.
 
Why do I think this? Well, in Mega Man X5, we hear Sigma say this about Zero:
 
I met an old man who knows a lot about you… He told me an interesting story. He told me that you are something far greater than what you appear to be… On his advice, I scattered the Virus so that it could infiltrate you, but you haven’t shown any signs of waking up…
 
Then, in Mega Man X6, we’re introduced to a new character, Isoc, a mysterious reploid with a genius-level intellect. He succeeds in convincing Reploids to join him to help fight the Nightmare Virus. But surprise, he’s actually working for the bad guy all along! Sounds an awful lot like another scientist who frequently tricks the world into thinking he’s not the villain, doesn’t it?
 
Oh, but it gets better. Isoc also seems to harbor a very strong hatred of X, referring to him as an “ancient piece of junk.” If Zero is the one who defeats Gate, you get a where Zero hears a voice near Isoc’s deactivated body, saying that he believes Zero is the strongest robot.
 
So not only does Isoc hate X utterly, he also believes Zero, Dr. Wily’s last and greatest creation, to be the ultimate robot.
 
What I’ve concluded from all of this is that there’s a good chance Isoc is Doctor Wily, who somehow managed to transfer his consciousness into the body of a reploid. And given that Doctor Wily helped create Zero, it then only makes sense that he’s the one who repaired him between X5 and X6.