By using information from Vector Sigma downloaded to the Key, Jack restores Optimus's memory. Optimus Prime unleashes the Matrix of Leadership, but at the cost of losing his memory, thereby allowing Megatron to manipulate him into joining the Decepticons' ranks.

The Autobots and Decepticons eventually make the startling discovery that Earth is in fact the body of Unicron, forcing them to ally and prevent his consciousness from reasserting control over the planet. After Megatron's revival, Starscream flees after repeatedly showing he is unable to prove his loyalty to the Decepticon leader.

Megatron returns, having discovered Dark Energon, which grants him the power to resurrect the dead, but is injured, with Starscream taking command in his absence. When the Decepticons resurface, the Autobots take three teenage witnesses, Jack Darby, Miko Nakadai, and Raf Esquivel under their protection. However, the presence of Transformers on Earth is not generally known among the civilian population. Autobot Central Command is located in a converted missile silo in Nevada provided by the United States government, with Special Agent William Fowler acting as their liaison. Team Prime lives on Earth, three years after their last confrontation with Decepticons.

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