Agent Fowler drives out of a military base, listening to a few tunes, when a semi truck begins to tailgate him too close for comfort. Fowler realizes that it's more than a case of road rage when the truck rams him. Fowler notices a familiar symbol on his attacker's grill- the Autobot symbol. He contacts the Autobot base, where Optimus Prime is not present. The apparent Optimus Prime continues to attack, and as Fowler comes upon a bridge, he pushes his car through the divider, where it hangs precariously. The Autobots receive his message and bridge in, causing Prime to flee and Arcee to give chase. Bumblebee catches Fowler's car as it falls, but the bumper detaches, and Bulkhead catches it before it hits the ground. Arcee comes upon Optimus, but is knocked out when he runs her over.
The next thing she knows, she's back at base, being checked up on. Ratchet doubts Arcee's assertion that Optimus ran her down, and the big 'bot arrives at base. The team goes on guard, but as Optimus offers proof that he's been at an underground energon site, the team stands down.
The other "Optimus" drives full speed into Alden Military Base, wrecking helicopters and prompting chase until he stops. As soldiers surround him and open the door to find no driver, he transforms and aims a weapon at them. Speaking in Prime's own voice, the double clearly announces himself as Optimus Prime, leader of the Autobots, before laying waste to the base around him. The other Prime tears through lines of soldiers, prompting Optimus, Arcee, Bumblebee and Bulkhead to bridge to his position. The fake retreats, and arriving military helicopters fire on the Autobots. They retreat to base.
Fowler fields a call asking about the attack, and receives the news that all Transformers, regardless of allegiance, are to be shot on sight. The team realizes that MECH has finally succeeded in replicating Cybertronians, inside and out, using human-made parts after studying Transformer anatomy so carefully.
Meanwhile, the false Prime arrives at a MECH bunker, where it is revealed that the robot is a remotely operated drone unit, with Silas in the control seat, expressing extreme satisfaction at the test run.
In attempting to locate the MECH base, Optimus notes that, unlike them, the duplicate (dubbed "Nemesis Prime" by Miko) must rely on its vehicle mode to travel, having no access to a Ground Bridge. This places its lair within driving distance of both incidents, giving a range for them to search. The 'bots fan out, and Bumblebee comes upon a large complex. Optimus and the rest plan to rendezvous at his position. He enters, while Silas watches him. He powers up Nemesis Prime and sends it out. Bumblebee is briefly fooled by the fake until Silas slips and reveals he cannot understand Bumblebee's speech. The scout attacks but is quickly overpowered by the more imposing robot.
The rest of the Autobots enter the compound, cautious of any lookalikes. Bulkhead and Arcee are both taken out individually, leaving Optimus for the final showdown with his doppelgänger.
At base, Ratchet attempts to isolate the control frequency of Nemesis Prime to pinpoint the location of its operator. He does, and Fowler insists on bridging in, citing that he is the one best equipped to deal with the "human element".
Nemesis squares off against Optimus, showing equal strength and agility. Fowler bridges in, and makes for the control bunker as the two Primes continue to spar. Nemesis catches Optimus, and shoves its blade into the Autobot leader. Silas gloats, commenting that he cannot feel pain through the robot, unlike his opponent, and revealing his intentions to build an army of these soldiers, when Fowler enters. They spar as well, and Fowler falls to Silas' superior hand-to-hand combat skills, only to reveal that he was just buying time for Optimus to beat the now-directionless copy. The real Prime dominates Nemesis, and their fight collapses the ceiling of the bunker, sending Silas's creation and a ton of rubble crashing down on top of him, putting Nemesis Prime out of commission in the process.
Optimus meditates on MECH's seemingly impaired functionality, now that it lacks a leader. However, Fowler brings him troubling news — in the pile of wreckage, no body was found.
Elsewhere, a group of MECH scientists monitor Silas' condition, noting that his injuries are terminal by normal standards — yet MECH is anything but, as they have the body of Breakdown all wired up to their leader.
- With the construction of Nemesis Prime, MECH has finally yielded results from Project Chimera.
- MECH has Breakdown's reassembled remains, which they collected after Airachnid killed him in "Crossfire".
- Ratchet recalls MECH's study of Breakdown in "Operation: Breakdown".
- Optimus claims he was away at a subterranean Energon deposit and pulls out a shard to prove it. This throwaway line would actually become a continuity note two years later, when the Rescue Bots cartoon would have Optimus show up to mine Energon with the Rescue Bots in the two-parter "What Lies Below"/"What Rises Above". In these episodes, they got trapped deep underground, which would explain his "out of communication" statement. Despite the distance in airdates, the timing matches up pretty dang well in in-universe chronology!
- Optimus recalls the theft of Starscream's T-Cog, which they learned about in "Crossfire" after it happened in "Operation: Bumblebee, Part 2".
- Silas took a scan of Optimus at the end of "Convoy", which is evidently how he was able to produce a nearly-identical copy of him in this episode.
- Optimus's right sword, which was broken in "One Shall Fall" and last seen still broken in "Orion Pax, Part 3", has been repaired at some point.
- This is the second time Bumblebee has tried and failed to save a car on screen. Only this time, someone was inside the car when he loses part of it. The first was "One Shall Rise, Part 1".
- As this is Fowler's first time in the Ground Bridge, he experiences nausea, similar to the effect on the children in "Darkness Rising, Part 5".
- The other bots should have known from the eye color that Nemesis Prime was not Optimus.
- Given Optimus' longer lifespan and thus greater combat experience, he should have mopped the floor with Nemesis Prime.
- When Optimus pushed Nemesis Prime close to the pipe he was wearing the mouthplate but for a second it looked like the normal face when the latter reached to the top he had the mouthplate back on.
- As Optimus returns to the base from the subterranean Energon deposit, for all but a brief moment, Bumblebee's chest does not look like it has fully rendered correctly.
- Agent Fowler listens to "The Touch", a song written for the 1986 Transformers Movie.
Main Article: Nemesis Prime (episode) Gallery
Nemesis Prime (episode)}}