So, these lines?

"I cheated, the lies that I told
Is for a future that I have seen
The death, the lives that I stole
The end has to justify the means"

This may be a strange question. But when is this song? Is this after he's stolen Gamma? It sounds like, in the beginning, he's a new man. He's upset with what he has done until the "Tell me why I'm the one they fear" line. It seems like that's a turning point. He steals Gamma, then goes on to say the "I cheated..." verse.

Also, is it possible that verse is actually Wily realizing that what he plans to do, or has already done, does not justify his seen future?

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I'm inclined to believe the song takes place at one specific point in time from a singular viewpoint and isn't a chronological sequence of events showing any kind of change in Wily.

Pretty sure "the end has to justify the means" indicates that he believes whatever he has done IS still justified... but that the price was great enough to almost make him question himself. Wily's not a bad guy, after all.

I think he's not reformed but simply gone crazy and now believes he's better than he is and more of a good guy.

The real question, I think, is motivation. What is Wily's motives? From a standpoint in the games it's simply ruling the world through superior firepower. I mean the plot of 6 was simply him stealing other countires war machines to take over the world. But we know he's not reformed because he sabotaged the robots he built with Light from the get-go. The first four Robot Masters in 3 stole parts of Gamma and Mega Man had to retrieve them. While Mega was busy, Wily stole Gamma. So it's hard to for me to even picture Wily as anywhere near reformed.

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"I want to be the one to fight against you, Dr. Wily~

Megas canon is slightly altered from game canon.

Megas Wily has always been more of a sympathetic character trying to create freedom/a future for robots rather than just some evil douchebag bent on world domination for selfish reasons.

I think Wily truly envisions a future in which robots are free, and he believes that he is the person who must lead this new world. He really feels bad for what he has done, but he is trying to convince himself that it will all be worth it when his vision has been achieved. He revived Protoman in the hopes that he would help the cause, but Protoman has his own plans. Now he is awakening Gamma in a last desperate attempt, only to see that he can't control Gamma either. It seems like Wily is alone throughout the song so I don't see any reason for him to fake it. The only thing that suggests otherwise is the first verse which could just be him talking with himself or bargaining with a higher power or something.

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"This news has just filled my heart with rainbows!" -Ghirahim, Skyward Sword

The end has to justify the means

He sees what a mess he has created, and knows the only way to justify all that he has done is to bring about such an utopia that will justify everything that has happened in order to redeem himself. Brilliant.

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To be honest you could argue that that is, in fact, how he is. I read an article a while back that actually painted Wily as a good guy with Dr. Light/Mega Man being a dick.

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Rest in peace Trevor

speaking simply from a commentator point of view It's truly a masterpiece. Speaking from a nit pick sort of view I think it kind of hops back and forth a little bit with it in the way that it's the activation, back into the whole "The end justifies the means". Deal, but that's just my ramblings lol

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~Memento Mori~

Alright, so I've been thinking hard on what gamma being "out of control" really means. It's hard to say for sure, but some of my thoughts on Spark Man recently got me to thinking:

What if Megas cannon Wily never intended to exterminate humans. What if his goal was eventual harmony between humans and their equals - robots? That type of end would be very justifialbe (to him), even if it did require war.

Before he activates Gamma, Wily makes this decision. He needs to continue, for the sake of the robots. As bad as it makes him feel, even though he is a murderer, he has to keep going. For robotkind's sake, as well as humankind's long-term survivability.

As he activates, Gamma makes his 'peacekeeping calcuation'... And you know what the result Wily hears is? The one he's always feared. The only way to achieve peace is the extermination of all humans (maybe even Wily himself)

Gamma is not out of control in the traditional sense of "berserk". Gamma is doing exactly what he was intended to do: Make absolute peace. The thing that frightens Wily is what that requires... Gamma is out of control only in the sense that its programming requires it to do something no one wanted.

This leaves Wily still in control, and closer to achieving his 'ends' than ever before.

But at what cost?

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Really it's hard to say since we don't know how far the Megas cannon stretches. In the latest Mega Man series ZX harmony has been achieved as humans and reploids are so alike most can't tell a difference.

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"I want to be the one to fight against you, Dr. Wily~

That's exactly what I was thinking except for when you said that Wily is still in control. I think once Gamma decides to kill everybody, that's what it is going to do regardless of what Wily does. That's why Wily says that Gamma is out of control. Especially since you pointed out something that I hadn't even noticed: Wily is human too, so who says Gamma won't go after him.

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"This news has just filled my heart with rainbows!" -Ghirahim, Skyward Sword

Food for thought. What if...

Drs. Wily and Light are working on Gamma.
Light has peace keeping orders preprogrammed into Gamma.
Wily steals Gamma and removes Lights idea of what it right and wrong.
He does this so that Gamma can choose the best possible way to enforce peace.
Gamma sees that humans are a threat to humankind.

Ironic huh?

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Rest in peace Trevor

I don't think Wily even needed to change anything. Light had programmed Gamma to figure out to achieve peace and extermination was the only solution that Gamma came up with, because as you said "humans are a threat to humankind." Light might have even known that Gamma would come to this conclusion which would explain chaining him in the first place.

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"This news has just filled my heart with rainbows!" -Ghirahim, Skyward Sword

Well Light also was also responsible for X and he had to seal him away so that his conscience could develop or something along those lines. Gamma may have been prematurely released.

The reason I mentioned Wily removing Lights "chains" is all of the robot masters have some pretty dynamic personalities. I'm not saying that he really did remove programming that light did but I could see it as Wily freeing Gamma from the tyranny of humans. Gamma should be free to do what it believes it should, not to follow the orders of a human.

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Rest in peace Trevor