Optimus Prime reflects on the responsibilities of all advanced races to spread freedom and peace, and laments that all the Cybertronians have spread is war. The Autobots have been in hiding amongst the humans for the last two years as Earth's cities were rebuilt following Megatron's planet-wide assault. Ratchet, Streetwise and Prowl are in their alternate modes, watching for signs of any trouble: trouble that comes as Breakdown destroys a power station in search of energon.

The attack is monitored by Skywatch control, and Spike Witwicky orders his forces to capture the invader. Breakdown is set upon by Spike and several other personnel in armored crash suits, built using stolen Cybertronian technology. Prowl and Streetwise are amongst the human police on the scene, and watch as Breakdown is immobilized and forced into his alternate mode by Skywatch forces. When they bring out their lethal particle cannons, apparently to destroy the Decepticon, Prowl can watch no longer and transforms, only to be brought down in turn: Spike had intended to draw him out all along. As he and Breakdown are driven away, Streetwise contacts the other Autobots...

At Autobot base, Wheeljack has engineered a counter to the inhibitors, and Optimus Prime orders him to fit them to their remaining forces. Hot Rod questions Prime's leadership, particularly their presence on Earth and the corresponding loss as more of their number are captured. Prime reiterates the need to protect Earth in case of possible Decepticon attack, but allows Hot Rod to stage a rescue mission to retrieve Prowl; he assigns Ironhide to go with him.

The rescue attempt goes poorly when it is revealed that Prowl was bait in a Skywatch trap; although Hot Rod's team rescues him, Ironhide dies leaping into a blast meant for Hot Rod. Optimus Prime grieves for his friend, and in a speech to his fellow Autobots removes himself as active commander.

Alone and ruminating on the end of the war and the new era in which they find themselves, Optimus Prime drives into the desert and into a Skywatch facility. As soldiers surround him, he raises his hands in surrender...

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