The first Zone of the Enders did this with the freaking LAST BOSS!

After you beat what you think is the last boss that you have been after for most of the game another person suddenly appears out of nowhere, reveals he's the boss of the boss you just killed, and fights you. His life bar is basically just for show, you literally can't even touch him.

You can't just let him beat you either, you have to survive long enough for backup to arrive and help you escape. In ZOE2 within the first half hour of the game you fight that same boss again, and he's untouchable again, this time though all you can do is get your ass kicked. You do finally kill him as the last boss of ZOE2 though, but you are playing as a different character in ZOE2, the main character from ZOE1 never gets to beat him or even participate in the final battle even though he is in ZOE2.