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as does the tag team duo of the Abrahamic god and devil.
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Oh, you.
EDIT: Also Alex in Golden Sun takes the cake for being a Magnificent Bastard.
Throughout the series he continually plays at least three sides against each other (Despite being a late player in the game) to very nearly become a victorious God over all. Only brutally stopped at the end by a Pound of Flesh Twist which left his fate open to interpretation by the players.
You first see him in the first of four lighthouses you have to stop the bad guys from lighting (Who are actually just playing into Alex's hand) where he is introduced as a pretty unspectacular minor villain whose only real powers are healing and teleportation. He outlasts the main villains of the first game however and very early on in the second game it becomes apparent that he's manipulating you and the new (false) bad guys with ease, going so far as purposefully healing your party before a climactic battle at the third lighthouse so you can fight the villains at good strength and then appearing after the battle with them and threatening your weakened party with destruction if you don't let them escape. He then disappears and isn't heard of till the end of the game where it is revealed that he set events in motion so that he would be at the receiving end of the lighthouses power and to make matters worse, to save the world you have to defeat the final boss and give him what he wants.
Also he manages to be a fantastic villain without spilling a drop of blood the whole way through both games, which merits him a distinction in its own right.