May not apply, exactly, since he doesn't start out a bad guy or boss, but I'd nominate Prince Rurik from Guild Wars: Prophecies.
Prince Rurik is the son of King Adelbern and heir to the throne of Ascalon. Dad makes some bad decisions during the Charr Invasion, gets killed for his trouble, Ascalon and her people are basically decimated. Prince Rurik (along with your heroic party) leads the surviving Ascalonians out of the devastation and across mountains through dwarven territory. He gets killed holding off some bad dwarves while you lead the people on and that's basically it for Rurik -- or so you think.
Much, much later, very nearly at the end of the game, he unexpectedly pops up when the big bad (a Lich) resurrects him (why and how said lich ever found the body, since it's presumably buried under tons of ice and snow on some mountains far, far away, who knows) and forces his rotting corpse to defend said lich against you.
It's a half campy, half WTF? moment. By that point the story -- such as it is, telling a coherent story has never been Anet's strong suit -- has taken several left turns and Rurik,the Ascalonian refugees, and all that has long since stopped being relevant. Still, it's quite memorable and, at least the first time through, not an easy fight.
Prince Rurik is the son of King Adelbern and heir to the throne of Ascalon. Dad makes some bad decisions during the Charr Invasion, gets killed for his trouble, Ascalon and her people are basically decimated. Prince Rurik (along with your heroic party) leads the surviving Ascalonians out of the devastation and across mountains through dwarven territory. He gets killed holding off some bad dwarves while you lead the people on and that's basically it for Rurik -- or so you think.
Much, much later, very nearly at the end of the game, he unexpectedly pops up when the big bad (a Lich) resurrects him (why and how said lich ever found the body, since it's presumably buried under tons of ice and snow on some mountains far, far away, who knows) and forces his rotting corpse to defend said lich against you.
It's a half campy, half WTF? moment. By that point the story -- such as it is, telling a coherent story has never been Anet's strong suit -- has taken several left turns and Rurik,the Ascalonian refugees, and all that has long since stopped being relevant. Still, it's quite memorable and, at least the first time through, not an easy fight.