During the Great Exodus, Megatron rallied his Decepticon armies to form a crew to man the Nemesis out of Trypticon on a mission to intercept and destroy the Ark at all costs.
Once they caught up with the ship, Megatron immediately ordered the boarding parties to attack it through cable tubes. Many of them were either killed or went overboard in the chaotic battle.
When the black hole dragged the Ark and The Nemesis inside, the crew have managed to survive the catastrophe.
The ship was used as the Deceptions's main means of transportation on the planet. At one point, the ship gained a mind of its own when Megatron used dark energon to fix it. It soon put the Decepticons and Autobots in stasis and set off to claim the Iacon relics. However, fourhumans managed to stop its plans and render the ship lifeless once again.