The Last of Us' Joel turns into the scourge of humanity by the end of the game, but knowing what he lost 20 years ago and what the world asked of him 20 years later, I don't blame him for wanting to be happy again. Making both times similar to each other in time of day and location and having similar killers was a nice touch without being overt about him having horrible flashbacks.
Shadowrun: Dragonfall's Vauclair's a war veteran, having witnessed the destruction of parts of Germany at the hands of the dragon Feuerschwinge. With the dragons in power over the world both physically and politically, humanity, in his eyes, had lost control over its own destiny. And so, he sought to correct that, regardless of what he had to do to achieve it in what little time he had left.
Watchmen's Ozymandias saw the Cold War ending all of humanity. In order to stop that, he had to create a new enemy, one so great that the world would have to unite in order to stop it. In order to do that though, he would have to stop the other Watchmen from interfering. Lying to some, framing others, the death of The Comedian: All in the name of the greater good as he felt there was no other choice and, well, there really was none.
Bonus: I wouldn't say I sided with them, but Radiant Historia's Heiss was asked, for a ritual to halt the decay of the world, to sacrifice the one person who meant the world to him. Instead, he chose to sacrifice the world, feeling there was no hope for humanity if delaying was the best they could do, setting up the plot for the game in the process. He was a cool villain, but it only really showed in the extended ending and, in that, he does something very un-villain like.
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