Quickstrike is put to trial for his betrayal of Megatron, but it is interrupted when the Vok send Tigerhawk, a supernatural fusion of Tigatron and Airazor, to stop Megatron's interference with time. They do not realize, however, that Megatron has part of his predecessor's spark within him, thus destroying him would cause another timestorm. Upon his arrival, Tigerhawk destroys the Predacon's ship. Tarantulas captures Tigerhawk and proceeds to kill his Vok control. The experiment goes fatally wrong however, and Tarantulas is killed. The sparks of Tigatron and Airazor reunite with the body of Tigerhawk and he is welcomed back home to the Maximals.

The Nemesis has proven to be powerful and dangerous under the now-insane Megatron, killing both Maximals and Predacons alike. Tigerhawk is destroyed with a large energy cannon, and Inferno and Quickstrike both get killed in Megatron's whimsical attempt at taking out a group of proto-humans. Optimus fights Megatron alone, while Dinobot II decides to aid the Maximals by sending them data about the Ark (a consequence from his spark now being independent, which apparently allows him to think more for himself and like the original Dinobot, though the episode hints that Dinobot II has become a conduit for the memories of the original Dinobot from beyond the grave as he recalls the last words spoken to the original Dinobot from Code of Hero, though this is never outright confirmed. However the clone loses the metallic echo his voice originally possessed upon his creation and begins to show signs of Dinobot's personal code of ethics, citing the concept of honor, which up until that point the clone did not care about, to Megatron when he is about to unleash Nemesis' firepower on a single proto-human after physically stopping him from opening fire on him). The Maximals receive the data and discover an Autobot shuttle in the Ark, which Rhinox flies and crashes into the Nemesis control tower, taking out Megatron as it goes all the way through both sides. Optimus flies away while Dinobot II bids farewell and goes down with the ship. The Nemesis is now out of control and flies off toward South America, where it would be discovered during the Great War. The Autobot shuttle and the Transformers on board are safe to resume their original place in time. The Maximals return to Cybertron triumphant with Megatron as their prisoner.

In a deleted scene, Optimus rips the original Megatron's spark from Megatron's chest and restores it within its rightful body.

Meanwhile, Waspinator, who quit the Beast Wars last episode, is shown to be worshipped by the protohumans, and declares he is "happy at last".