The Mutagen Bomb was a device seen in flashbacks during the episodes comprising of the Raphael: Mutant Apocalypse story arc. One day, it lifted into the air and detonated, and it either mutated or killed all of the humans. Mutants that were close to ground zero also seemed to have been mutated a second time.
The Kraang logo was shown on the bomb, but it was not revealed who or what instigated the attack.