More like both have their own methods, parallel branches along the same tree. Recall, if you will, that even without Dark Elf (one of many Sigma Virus derivatives), Omega still resonates the same energy signature as Dark Elf.
I'm not convinced that Wily is "failing" with Zero. He aptly demonstrated in X6 (and is further implied in X4) that if he wanted to capture Zero, nothing's stopping him. For some reason or another, it seems to me that he wants to take a more passive role.
But he contained a flaw in his cognitive program that made him violent and unwilling to obey instructions, so Dr. Wily himself sealed Zero in a capsule.Zero contained a flaw in his cognitive program for which Wily sealed him. That is Wily at the beginning failing to properly complete Zero's cognitive program. Wily has found a way around that with X2 and X5, but initially he seemingly didn't. Dr. Vile on the other hand, has no problem reprogramming a virusless Zero to become his slave. Which is rather surprising with Wily's own initial problems, and the mental instability of such copies as the Zero Nightmare. But then, we do not know the mental state of X2's copy, and TvC's Zero vs Zero battle also seemingly has both Zeros equally sane.
In what way does getting one's ass kicked by X constitute losing the virus? We know from Alia that "killed" qualifies under that, but not so with merely "beaten".
Then it begs the question of how we describe Techno's, Doppler's and Gate's return to normalcy after getting beat up by X. But, maybe Zero works completely different than regular Repliroids? After all, the piece of DNA Gate found was spreading the virus like crazy.
Iwamoto's X2 Zero vs X scenario had X punching out a Sigma Virus chip within Zero's head lens (Z-brain?) and so returning Zero to normalcy. This scenario works very nicely with what we see in X2 the game. But compared to X5, in which we can't really establish a loss of the virus by beating up Zero, maybe we should at a different reason for his suddenly sacrificing himself for X? Was that Hunter Zero, or actually the awakened Zero giving up his life? More on that a few quotes below.
I'm not convinced of that.
Zero and Sigma's change in allegiance represents "circumstances can change anything". Ergo, not as planned. There may be some planned aspect that worked toward it, but it was not intended in that way, at that time, with those results.
Might also go a ways to explaining how nobody at Hunter Base noticed.
I just wonder what that means for the poor smuck that has to repair the virus spreading damaged Zero. Considering the difficulty of that, maybe the human Cain did it all the time?
If the Hunter personna was established as permanent, others should be able to be written as permanent as well. If it is indeed the ideal state for Zero to learn new abilities, then that would lend more credit to such a fall-back upon defeat as being intentional.
Zero's Hunter Person might be "ideal", but its lack of order input would not be. Wily has no control over this Zero, but he certainly seems eager in keeping that brain chip. Inafune specifies that change to good as circumstance; Zero should still remain evil. But the evil Zero's personality isn't really that different from the Hunter Zero; only the person that is his reason for fighting has changed. Which goes a long way to explaining how X5's awakened Zero actually sacrificed himself for X; fighting for X and fighting for Wily. With Sigma trying to kill X with the battle of destiny yet incomplete, what is best for both X and Wily coincide. Sigma himself threatened Wily's rivalry then and there.
I took notice that virtually nobody seems to actually believe in Sigma's cause.
Spark Mandriller?
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