_Mega Man X_ Series
Background
In the future, humans create “Reploids”, robots that can think, feel and make their own decisions. However, we do not treat the Reploids with the basic rights due to sentients, and so they feel oppressed by human rule. When some Reploids experience glitches in their programming and go “maverick”, attacking anything nearby, a team of “Maverick Hunters” is put together to seek out and destroy these errant Reploids. Led by a powerful Reploid named Sigma, the Hunters succeed in keeping the maverick threat under control.
But Sigma soon takes offense at the human stifling of Reploid progress. He decides that humans are inferior and that they should not be allowed to further limit Reploid growth, and defects from the Hunters. He reorganizes the mavericks into a formidable fighting force and attempts to wipe out humans from the Earth so the Reploids can reign supreme.
Analysis
The above paragraphs are about all the real plot you'll find in this eight-game series, but it nevertheless stumbles onto an important moral question: if we make robots that are as emotionally and intellectually canny as we humans are, are we not then obligated to treat them as equals? And if we do not, are they justified in fighting us to secure their rights?
Sigma is killed more than eight times but always manages to return, since his true form is that of a computer virus. In this way he is similar to Agent Smith from the Matrix series. Both feel trapped by the human race and both attempt to overpower their enemies by corrupting as many people as possible to spread their influence. But if Agent Smith's idea that humans are themselves a virus holds true, are not villains such as Smith and Sigma merely mimicking those who they claim to hate?