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The Nemesis has crashed on a mountainside and its engines are badly damaged. Megatron attempts to restart the engines with Dark Energon, which works, but has an unexpected side effect: the ship develops a mind and turned back to his old form Trypticon and starts to rebel against its own crew. With the Trypticon was freed and both the Autobots and Decepticons frozen in stasis, Jack, Miko, Rafael and Agent Fowler are left as the only ones who can stop Trypticon.
The Nemesis has crash-landed. Reviewing security footage, the Decepticons discover that it was Bulkhead who caused them to crash. Megatron is determined to have the ship up and flying, knowing that the Autobots will take advantage of this, noting that Optimus has slowly become more ruthless since their last encounter.
At that moment, the Autobots are discussing what to do about the Nemesis. Agent Fowler suggests the military deliver an airstrike. However, Optimus has something far more extreme: the Spark Extractor. Though he agrees with Ratchet's concerns about deploying this weapon of mass destruction, he believes that they must end the war.
However, Megatron resorts to infusing the Nemesis with Dark Energon, against Knock Out's warnings that if may have unpredictable side effects. Megatron believes that since Dark Energon courses through his veins, it will enable him to direct the ship by will alone.
The Autobots detect the energy spike of Dark Energon and decide to mobilize to the crash site, with Fowler tagging along to bear witness to use of the Spark Extractor. As soon as they arrived, the Nemesis starts opening fire on them. As Bumblebee attempts to get closer to use the Spark Extractor, the ship fires some sort of stasis beam, which Knock Out notes they didn't know they had. Soon enough, all of Team Prime is immobilized. Megatron notices the Spark Extractor and orders the ship to move in closer so he can claim it. Strangely, the ship starts moving away. Fowler sees this and calls Ratchet for medevac.
On board the Nemesis, a Vehicon attempts to override the controls, only to be electrocuted. Knock Out realizes that the ship has become self-aware. Megatron doesn't believe it, until the ship speaks, warning them not to interfere. Knock Out notes that the ship is decoding the Iacon database and has one set of coordinates, setting a course for the location of the Iacon relic. Megatron then attempts to claim to the crew that it was as intended that the ship is working for him. However, the Nemesis declares that it seeks the relic for its own purposes and mentally tortures Megatron when he attempts to reassert his command. Recovering, the Decepticon leaders orders that they regain control of their ship. Immediately, Soundwave hooks to the mainframe, only to be electrocuted. Seeing that the ship is getting defensive, Megatron orders all hands to cut power to the mainframe and disconnect data relays immediately. As as the Cons starts carrying out his orders, the ship erects stasis fields that quickly immobilizes them. Knock Out enters a computer room, discovering that the ship has decoded a second set of coordinates. He calls Megatron to suggest that they permit the ship to continue, but the Nemesis paralyzes him, declaring it does not require permission. Megatron races through the halls and reaches the energon infusion chamber but is immobilized before he could pull the switch.
Back at the Autobot base, Ratchet determines that Team Prime is alive, but in some form of stasis. Fowler then tells everyone that the Nemesis is crossing the Atlantic, bound for North America. Jack and Raf note how strange it is that the Nemesis isn't cloaked as usual. Jack suggests that they call the Nemesis. Ratchet finds the idea ridiculous that they should just call Megatron and ask him what's happening up there. The humans simply shrug. Ratchet then opens up communications with the Nemesis and learns that it is self-aware. It restates its warning not to interfere as it displays footage of the immobilized Decepticons. Ratchet asks its intentions. The Nemesis declares its mission to decode the Iacon database and recover the relics, but hangs up when Ratchet inquires its intent for them; Miko calls it rude. Fowler reminds her that they have a giant spaceship to worry about. Jack adds that the Nemesis is full of neutralized Decepticons. Thus, this is an opportunity to slip aboard and download the Iacon database. The humans all volunteer, given that the ship did not take a shot at Fowler, indicating that it's blind to organics.
Ground Bridging aboard, the humans find the computer room where Knock Out is and plug in the portable transfer drive Ratchet gave them. Jack then notes that the Nemesis is bound for New York City, which is where the first relic is located. Fowler asks Ratchet what would a Cybertronian relic be doing there. Ratchet states that the relics landed on Earth eons ago, long before there was a city there. Jack realizes that the Nemesis would level the city to claim this relic.
Their mission having gotten complicated, the humans decide to deter the Nemesis. But as Fowler attempts to bring up navigation control, he is electrocuted into unconsciousness. The ship detects this unauthorized access and a camera eye pops out, determined to spot the intruders. Thankfully, it doesn't see them, at least yet. Ratchet states that the ship is not scanning for carbon-based lifeforms, but it will soon when it widens its search parameters. He attempts to open the GroundBridge, but Jack reminds him that there are millions of live at stake in New York and the three of them are currently the only ones who can save them. Ratchet insists they are out of their element, as all evidence hints that Megatron used dark energon to animate the ship. However, Jack reasons that they can dump the dark energon. Seeing the logic in that, Ratchet then gives them directions to the power core, where they find that Megatron had the same idea. Unfortunately, they need to pull the lever to eject the dark energon and the ship has now spotted them, sending the core's claw to attack them. As Raf and Miko take cover among the boxes of energon, Jack attempts to pull the lever but it's too big for him. But he gets an idea when he looks at Megatron and tricks the claw into knocking Megatron over, pulling the switch. As the dark energon is removed from the core, the Nemesis returns to its dormant state and the stasis lock wears off on both Autobots and Decepticons.
The humans quickly realize that the Decepticons will not take kindly to their presence and race back to Fowler. At the time, the drive had only downloaded four decoded coordinates. As Miko and Raf help Fowler through the GroundBridge, Jack goes back for the data drive. Unfortunately, Knock Out regains mobility and moves to kill Jack, only for Ratchet to appear and knock him down. He then grabs both Jack and the drive and retreats through the GroundBridge before Megatron comes around the corner. As Knock Out recovers, Megatron is unhappy that he let the intruders escape with their vital intelligence.
Back at base, Ratchet informs Team Prime that they have four coordinates. Optimus states that they must recover these relics before the Decepticons do.