- "Look doc, I don't plan on dancing with any bots, but there's a human element in play here. And in case you haven't noticed, I happen to be a highly-trained, government-grade, human." Agent Fowler
On the road listening to a familiar tune, Fowler is suddenly attacked by what seems to be Optimus Prime, who's trying to run him off the road. At the Autobot base, the toy car race between the 'Bots and their kids is cut short when Ratchet is alerted to the situation. The team rolls out, just barely in time to save a distressed Fowler from being run off a bridge by the truck. The mysterious truck retreats, with Arcee in pursuit, while Bulkhead and Bumblebee rescue Fowler even as his car falls of the cliff. Arcee is knocked out by the unknown enemy, and awakens at base sometime later. The 'Bots and Fowler report to Ratchet that apparently they were attacked by Optimus, which has some grounding considering Optimus isn't currently at base. However, their leader soon arrives, finding to his confusion a very, very tense and uneasy team. After nearly being shot at for revealing a chunk of Energon he found, he finally realizes something is up, but is able to calm down his men.
The mysterious truck forces its' way into a military base, and when cornered by the military and after the revelation comes that there is no human driver, he transforms into robot mode. The look-a-like introduces himself as Optimus Prime, before going on a devastating rampage and working to wipe out all military personnel present. The team quickly bridges out to face the fake, but are fired upon by US choppers, believing them to be reinforcements. The fake flees, as do the 'Bots. Back at base, despite his best efforts, Fowler is informed by his superior, General Bryce, that the US military is on orders to fire on any Cybertronian. Ratchet and Optimus deduce that MECH has finally succeded in creating a man-made Transformer, after their invasive studies on Bumblebee, Starscream and Breakdown. The fake Prime is revealed to be a remotely-controlled creation, directed by Silas, who is pleased at the auspicious test runs he's made.
Optimus observes that being a man-made 'Bot, the fake - dubbed "Nemesis Prime" by Miko, which does catch on with the team - has no access to a Groundbridge, and must be driving back to its' base whenever it flees. This narrows down the MECH base to somewhere around the area Fowler was attacked and the destroyed military base. That night, Bumblebee is able to find a complex where Silas is holed up, and the MECH leader quickly rolls out Nemesis. He's briefly able to fool Bumblebee, until he is unable to understand Bumblebee's speech, but nevertheless quickly downs the scout, and Arcee and Bulkhead just as quickly. Meanwhile, Ratchet's attempts to find Silas' exact coordinates are interrupted by Fowler, who convinces the medic to bridge him out to the field to take on Silas himself.
Nemesis and Optimus battle, but the former quickly gains the upper hand due to a lack of morality and pain. Just as Silas reveals his endgame of an army of these machines, Fowler arrives and distracts the gloating villain long enough for Optimus to recover from a lethal blow and take out his look-a-like. Nemesis comes crashing down from the roof on top of Silas, and Optimus and Fowler exchange thanks and a healthy respect for each other. However, the celebration is cut short later, as Fowler reports that no body was found in the ruins of the MECH base.
At some MECH labratory, a doctor informs that Silas' damage to his internal organs is massive and beyond the scope of traditional medicine, but fortunately for their leader, MECH is anything but conventional. The episode fades out on a shot of Breakdown connected to some machines by cords.
- Absentee Actor: Two Decepticons, Starscream and Breakdown, were mentioned, but no Decepticons appeared in the episode.
- Big Damn Heroes: How the Autobots save Fowler in the beginning of the episode.
- Bluff the Impostor: When Bumblebee infiltrates MECH's base, he is confronted by Nemesis Prime, pretending to be Optimus. Bumblebee had a surefire way to tell if he was fake or not.Nemesis Prime: Bumblebee. Be on your guard. My double could be anywhere.Bumblebee: (speaks in his native beeping sounds)Nemesis Prime: ... I'm sorry, what?(Bumblebee's eyes narrow and attacks Nemesis Prime)
- Color-Coded Characters: While it's pretty obvious to the viewers which Prime is which, nobody in-universe can seem to tell them apart.
- Curb-Stomp Battle: How Nemesis Prime easily takes down the Autobots minus the real Optimus.
- Dropped A Giant Transforming Robot On Him: At first, Silas looks like he's ready for an epitaph. However, the next scene shows him being hooked up to Breakdown's remains...
- Foreshadowing: Silas tells Optimus how MECH has made the perfect blend of man and machine. The end of the episode shows a mortally injured Silas being hooked up to the corpse of Breakdown with the intent of transferring his subconscious there.
- "Hey, You!" Haymaker: Fowler deliver one to a MECH guard.
- Impaled with Extreme Prejudice: Optimus gets gutted by Nemesis during their battle.
- It's Personal: The reason Miko thinks Fowler should be allowed to enter the fray.
- Mythology Gag: The music playing in Fowler's car during the Cold Open plays several riffs of The Touch.
- Spot the Imposter: Bee is able to figure out Nemesis Prime is fake because he can't understand Bumblebee's form of speech.
- Status Quo Is God: After a season of build-up and promises of some grand scheme, Nemesis Prime and Project Chimera are completed, but are taken out in the same episode.
- Super Prototype: In MECH's first attempt at building a transformer, they successfully build one that matches the most powerful one they've ever seen. This is especially noteworthy since Optimus is not one of the many 'bots that MECH captured.
- Title Drop: Miko calls the fake Optimus "Nemesis Prime".
- Villainous Breakdown: Silas, when he realizes that Agent Fowler successfully distracted him from the fight with Optimus, giving Optimus the chance to fight back. His normally calm demeanor slips as he loses control of the fight which ends with Nemesis dropped on top of him.