Remember that this is in context of the story. The writers may have written the story and how everything happens with a completely different view on it.
If the scriptwriter has a different view then that scriptwriter is factually wrong.
Only the mavericks in X8, plus a few exceptions, went maverick on their own will. Most reploids and mechaniloids before then went maverick by the virus as if they were possessed. The virus took over their electronic brains and controlled them.
I know, but that's what I'm complaining about... the real 'virus' that should be turning reploids against humans is the very thought that rebellion is possible, passed as a meme rather than a physical or electronic invader. But no, it's a virus... not that this makes any sense at all that a program code somehow takes physical form and causes direct attacks against hunters. Then again this is a game where robots can physically enter 'cyberspace' or whatever for several stages, so I guess making sense of this crap is a lost cause regardless.
Genetics and environment are strong motivations for a deterministic viewpoint, but the free will advocate has a lot of wiggle room left.
Only because the meaning of free will is being shuffled in different contexts between 'free to' and 'free from' depending on the circumstances. If we truely had free will we really could will anything (and there is a difference between willing and doing, which you neglected; a guy could will himself to fly all day without accomplishing anything), but the reality is that the things we will are determined by various factors of environment and nature... we might be able to DO otherwise, but we can't WILL otherwise to find out.
Now we do have
illusory free wills so long as no external, identifiable force is coercing us to behave this way because we are still doing what we will, and for this reason we are still responsible for our choices even if we couldn't
really choose otherwise. Justice is then predicated not on punishing the misdeeds of a rebellious will but rather on attempting to correct the internal workings of a person's decision making process through external stimuli so that future volitions will hopefully be more acceptable to society.
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Oh, and I've been playing through some of the old games since this topic reminded me how fuzzy my memories of those games is getting.
X1 - Chill Penguin
X2 - Crystal Snail
X3 - Blast Hornet
X4 - Split Mushroom