All this talk reminds me of a game I've started to work on using RPG Maker XP. It's basically Metal Gear Solid meets Die Hard, using a complex and powerful projectile-based action battle system.
So far, the characters include:
Vyx (anthro fox, heroine)
Dr. Solomon Bowman (scientist, creator of Vyx)
Colonel Daniel H. MacLeod (US Army colonel)
Maximilian Renard (leader of terrorist cell "Chimera")
The plot: The terrorist cell known as "Chimera" takes over Dr. Bowman's private genetic research facility in order to take control of the nanomachines used to induce massive genetic changes and threaten to contaminate the United States' largest natural reservoir with the nanomachines if their demands are not met. After a US Army strike team is neutralized by Chimera's elite genetically-modified "super-soldiers," the task of rescuing Dr. Bowman and neutralizing the terrorists falls to Vyx. Vyx finds out later on that the terrorist leader Renard has been planning to dump the nanomachines all along, and Chimera's demands were just a front. Here is a scene discussing Renard's motives. I plan on writing the script so that it raises the possibility that Renard was a good guy, not a villain:
Renard: So, you must be the wrench in our machine.
Vyx: I'm here to stop you from poisoning the reservoir!
Renard: Poison?
Renard: The technology that created you is a poison?
Renard: If it weren't for these nanomachines, you wouldn't even be here.
Vyx: The people in this country don't deserve to have this change forced upon them!
Renard: They don't?
Renard: You've probably spent your whole life sheltered here. You don't know what it's like-what people really deserve.
Renard: I've seen the lowest members of the human race.
Renard: And I've seen them doing horrible things.
Renard: I don't suppose Dr. Bowman taught you about the Ku Klux Klan?
Renard: Or neo-Nazis?
Renard: He probably never told you anything about Scientologists or pedophile priests.
Renard: There are people in this world who deserve to have these nanomachines force-fed to them.
Vyx: Why?
Renard: Why? To open their minds!
Renard: These people must be dragged kicking and screaming into the twenty-first century!
Vyx: I don't understand. All this will do is create chaos!
Renard: Of course it will. People will be afraid. Few will understand what's happening to their bodies, and nobody will know what water is safe to drink.
Renard: The people who will be affected the most, of course, are the ones who oppose this sort of thing.
Renard: Imagine if a bigoted, dedicated white supremacist woke up one day to find himself black. .
Renard: There will be chaos, there will be hysteria. There will be blood.
Renard: But out of this chaos will come a new order!
Renard: Old prejudices will be cast aside and people will be forced to realize at the most fundamental level that it's what's on the inside that counts.
Renard: It will be as close to a utopia as possible. A veritable heaven on Earth!
Renard: And you would deny me this dream? Why?
Renard: Because a man with some fancy medals pinned on his chest told you to?
Vyx: ...
Vyx: ...I can't let you hurt all those people. It's not right!
Renard: Not right? Not right?
Renard: They will all die someday anyway-but if I succeed, they will die sooner, and with a purpose.
Renard: Which is better, a death that is meaningless or a death that changes the world?
Vyx: ...
Renard: Your father probably never taught you anything like this.
Renard: In morality, black and white don't exist. There are only shades of gray, approaching the extreme ends of the spectrum but never reaching it.
Renard: Sometimes, terrible deeds can make the world a better place. Ends do justify means.
Renard: Now, will you join me?
Vyx: ...No.
Renard: I'm sorry to hear that.
Renard: You won't live to see my utopia.
Renard: And when you arrive in hell, tell your bosses that I said "hello."