Shepard, of the Mass Effect series, if you opt to play him/her as a Renegade. S/he's trying to save the galaxy, but s/he has no qualms with killing anyone who gets in his/her way to do so.
Garrus Vakarian in Mass Effect 2. By this point he's Space Batman.
In Mass Effect 2, even Paragon Shepard is antiheroic to an extent since he/she has to cooperate with a terrorist organization to fight the Collectors.
Miranda Lawson, one of the most loyal members of the aforementioned terrorist organization, joined it because she firmly believed that they were doing the right thing.
Thane Krios, an assassin on a quest for redemption.
Heck, most of the cast of the second game, apart from Tali and Jack.
Under Paragon Shepard's influence, even Jack shows signs of moving into Anti-Hero territory. "
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