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Agent Fowler is leaving military base when a semi-trailer truck attempts to run him down. He then spots an Autobot insignia on its hood and becomes confused, assuming the truck to be Optimus Prime. He contacts the Autobot base when at the same time, the Bots are watching the kids race remote control cars. Upon confirming that Optimus is conveniently out, he tells the Bots of his predicament, to their confusion. At that moment, the truck nearly drives Fowler off a bridge, had not the Autobots arrived in time and save him. Noticing the truck fleeing the scene, Arcee figures it's an imposter, as Primes don't run, and gives chase. She briefly loses her quarry before being blindsided by it.
Arcee wakes up back at base and correlates Fowler's claims. This puts worry into the children, asking why Optimus would attack Fowler. Ratchet doesn't believe it and goes to the sensor console to prove that their leader was nowhere near the incident. Conveniently, Optimus has just returned and takes note of their cautious expressions. When asked about his whereabouts, Optimus explains he was out of contact because he was in a subterranean energon deposit, as he produces the blue crystal. Fowler then explains
Meanwhile, the same truck bursts into a military base. Troops surround it and upon checking the driver's seat, they find no driver. Suddenly, the truck transforms into Optimus Prime, which then begins attacking.
Fowler then receives a call from General Bryce regarding "Prime's" appearance, which confuses him. He tells the Autobots of this occurrence and they groundbridge to investigate. By the time they arrive, the imposter transforms into vehicle mode and drives off. At the same time, choppers appear, assuming the Autobots to be hostile and open fire, forcing them to return to base.
Fowler attempts to convince Bryce that it was the impostor who attacked the base and he was with the real Optimus but his superior refuses to hear him. As he signs off, he tells everyone that the military is on a search-and-destroy Bot hunt. Optimus says this changes nothing, as this imposter Prime is a grave threat. And Ratchet suspects one group that could've created it: MECH.
At the moment, Silas is remotely piloting the Optimus doppelganger back to base and complements the flawless performance of the telepresence controls.
Team Prime theorizes that with MECH's studying of Breakdown, knowing that energon fuels Cybertronian and acquisition of Starscream's T-cog that they were able to create this knock-off of Optimus, which Miko dubs, "Nemesis Prime". Fowler asks where they should begin, for MECH's base could be anywhere. The Autobots say they can shorten the haystack a bit; while MECH has learned much of Cybertronian biology, they haven't absorbed their technology. Without access to a groundbridge, Nemesis Prime would have to rely on its vehicle mode for transportation and therefore, the MECH base may be in driving range of both incidents. Fowler is willing to help out but Optimus refuses him, not wanting him to get in harm's way again. Fowler reminds him that they can't just go out with the military on the hunt for them. Optimus assures him that they will maintain vehicular mode until absolutely necessary.
The Autobots then go on the search. Bumblebee scouts an abandoned plant, right where the MECH base is. Silas takes Nemesis Prime for a Bot-to-Bot rumble. He attempts to fool Bumblebee into thinking he's Optimus. But when he fails to understand Bumblebee's speaking patterns, he knows he's the impostor but is swiftly dispatched. The other Autobots come to the plant upon getting radio silence from their scout and split up. However, Bulkhead and Arcee are separately dispatched by Nemesis Prime. Eventually, Optimus comes face-to-face with his doppelganger.
Back at base, Ratchet manages to isolate the control signal to pinpoint Silas' location. Fowler quickly volunteers to take it out. Ratchet is hesitant, giving Optimus' warnings. Fowler argues that he doesn't intend to go after Nemesis Prime, but the human controlling it. Miko backs him up, stating that Fowler deserves some payback.
As Optimus does battle with Nemesis Prime, Fowler infiltrates the MECH base. All the while, Silas taunts Optimus, stating that Nemesis Prime is designed to be equal in strength and power and his reflexive training combined make it nigh-invincible. As their battle takes to the top of a tower, Silas impales Optimus, gloating that his puppet can't feel pain. As he readies for the final blow, Silas states that MECH will be unstoppable once they gain an army of Transformers.
Suddenly, Fowler surprises him after knocking out his guards. Silas distracts himself from the Bot battle to fight Fowler, who notes his opponent swiftly countering his attack, and asked if he's ex-military. Silas confirms he was Special Tactics and asks who Fowler used to serve with. Landing a few punches, Fowler boasts he was an Army Ranger. Silas notes from his physique and slow reaction time that he's a retired Ranger and knocks him down. However, Fowler reveals that it was not his intention to beat Silas in hand-to-hand combat, but merely to distract him. Silas then realizes too late and rushes back to the controls but is unable to counter Optimus' renewed attack. The Autobot leader then brings a slam on his doppelganger, causing the roof to give way and Nemesis Prime falls on top of Silas. As a trio of choppers come to investigate, Fowler tells Optimus to return to base while he sorts things out.
Back at base, Miko asks Bulkhead how it felt to have someone resembling Optimus beat the scrap out of him. He only groans while Arcee says it's a side she never wants to see. At the same time, Ratchet is patching up Optimus wound. The latter asks outloud where MECH will function without its leader. Fowler then informs them that they sifted through the wreckage and couldn't find Silas' remains.
In an unknown location, a MECH surgeon notes that the damage to Silas' internal organs is massive and beyond the scope of conventional medicine. "Fortunately for our leader, MECH is anything but conventional." The camera then pans to a shot of the remains of Breakdown.