I have a theory on how the season will end...
1) Brainiac eventually comes around and dies a heroic death to save one or both Supermen, mirroring the training sequence at the beginning of the season premiere.
2) Even more tragically, he dies as a villain trying to kill the others, which would mean that he doesn't go down in the heroic way he's always wanted to (as indicated by the training sequence, again).
But I'm sure he'll die. He's a robot, after all, so they can get away with it.