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Millennia ago, Nova Prime set out from Cybertron aboard his ship, the Proudstar, to find uninhabited worlds that could be cyberformed and colonized by the Transformers. However, the evil Unicron corrupted Nova Prime and his crew, who soon began attacking inhabited worlds in a monstrous quest; this eventually led them to Earth, where the Proudstar crash-landed. Many years later, the Decepticons under Megatron find the ship and begin using its power to fuel a force of Insecticons that they will use to cyberform the planet. As such, a small force of Autobots under Optimus Prime invades the Proudstar in order to stop the Decepticons' plan and recover information about Cybertron's history that has been lost since the beginning of the Great War.
Regrettably, the ship's automatic defenses eject the power core the Autobots seek to deactivate, and it is then seized by the Decepticons. While attempting to recover it, the Autobots are forced to engage the Stunticons in the form of Menasor, having previously battled Devastator. They then travel through a Space Bridge to Cybertron, where they confront Starscream and Shockwave before following Megatron back to Earth. Due to damage sustained earlier, the core ruptures and the Autobots are unable to deactivate it forcing them to seek out the ship's Ferrotaxis computer, which Megatron currently possesses.
After being forced to fight Menasor and Devastator yet again, Optimus and Megatron engage each other in a duel in space for the computer. Optimus is victorious but finds he is unable to use the computer to deactivate the Insecticons and is forced to destroy it, which shuts down the ship's power core and halts Megatron's efforts to cyberform the planet. Dedicated to now protecting their new home, the Earth, the Autobots set to work on a new project: Optimus Maximus. Unbeknownst to them, Nova Prime is in stasis aboard the Proudstar, and awakens as the game concludes.