Okay, thought that just entered my brain-parts while listening to the album last. I don't think this was intended, and this theory doesn't even really mesh with what I think of the rest of the album but I'm going to mention it anyway. Also, someone else may have come up with this already. I dunno, I didn't really bother to check.
SO, word on the street is that History repeating Red/Mauve/Hot Pink will take place simultaneously to Blue, showing Protoman's story unfolding alongside Megaman's. If that's true, then this song would take place near the end of both stories, rather than just Mega's. On top of that, there's the debate as to whether the cued explosion at the end was Megaman being shot and exploding, or Protoman destroying Light's lab.
Why not both? If this is the end of both stories, what if it was Light encouraging Megaman to go kill Dr. Wiley right in the face while, at the same time, Wiley is ordering Protoman to put an end to Light? What if they're both singing about how the other needs to die? After all, Wiley's wanted revenge since the first game (second album), so the song fits him too. That, and it seemed to fit nicely into the grey/grey morality that the Megas have been building this whole time.
That said, this is just a theory that I had, and not one that I'm even terribly fond of. If anyone likes the idea, awesome, you're welcome, etc. If you don't, well... also awesome. We should hang out some time.

Actually I think the last straw for Light was seeing Protoman as a war machine. Light loves all his creations, if he could I'm sure he would've rather saved the original six then destroy them.

I'm not sure that he did destroy them.

We know that the Megas plan to do some songs based on MM9 at some point, right? Well, in the game, at least, the original six are actually still around; repaired and returned to their original programming. In fact, when the MM9 robot masters begin attacking, the six of them try to stop them, but fail.

I know that doesn't hold a whole lot of weight, but I think it would make sense. Look at the original "I Wanna Be The One", from Get Equipped. At that point, Mega Man is still an idealist who talks about fighting for justice, even after the events of the first game. What I think went on is that Mega Man broke the original six, but then brought them back to Doctor Light's lab. Doctor Light being their creator, he was able to repair them, so there weren't really any casualties in that first conflict (aside from a few hundred Mettaur corpses, of course).

However, during the events of Get Equipped, Mega Man kills off MM2's Robot Masters. The important bit is that those eight were the first DWN models; Wily's creations, indepndant of Light. Doctor Light couldn't have repaired them even if he wanted to. I'm willing to bet that Mega Man didn't understand that until after Crash Man died. Like, I'm imagining the scenario would be that Crash Man blows up, Mega Man contacts Light and tells him that Crash Man is so damaged that he doesn't think he can be repaired, and Light tells him that repair was never an option. For any of them.

And so Mega Man learns that all this time, he was on a mission of extermination; he was built to kill.

As for this song, I think my favorite par might be the spoken bit, where he's talking directly to Mega Man. Especially "They
will forgive me... But I wonder, am I right to ask this of you?"

Wow, thanks, guys. Always feels good to have people like your theories. I honestly hadn't even thought about that angle until reading this topic, so thanks for helping me make that connection.

This board has the official manga I was talking about., in case you were interested.

...man, that being a semiofficial adaption of the game, I can just imagine how the Megas will do their take on it. I mean, it just about writes itself, doesn't it?

Back on the topic of the song itself, this song makes one line of "Walk Away From Light" very interesting:

"You say 'don't take their lives' / 'they don't deserve to die' / And who does? / Do you think it's us? / And what of the one who calls us sons / are you gonna kill him, too?"

Taking this song into account, we know that the answer is yes. Chilling.

... then use karate to save her from a group of bandits. If you have time do a sweet skate trick that causes manure to get all over Biff and his cronies.

Similar to the MM2 arc in the Archie comics series? Which is awesome by the way.

I haven't gotten to read to much of that series yet. I plan on picking up the graphic novels when I have spare cash that I'm not spending on conventions and stuff.