The Nemesis has crashed on a mountainside and its engines are badly damaged. Megatron attempts to restart the engines with Dark Energon, which works, but has an unexpected side effect: the ship develops a mind and turned back to his old form Trypticon and starts to rebel against its own crew. With the Trypticon was freed and both the Autobots and Decepticons frozen in stasis, Jack, Miko, Rafael and Agent Fowler are left as the only ones who can stop Trypticon.