Flying Mind is the eleventh episode of season two of Transformers: Prime, and the thirty-seventh episode of the series overall. It aired on April 28, 2012.
With the Nemesis down, Megatron discovers that an Autobot was responsible for the crash. Despite Knock Out's protests, Megatron infuses Dark Energon into the ship's power core, hoping its regenerative effects will cut down on the lengthy time it would take to get the ship airworthy. Meanwhile, the Autobots feel this might well be the time to strike. Optimus Prime reluctantly decides to use the Spark Extractor to terminate the Decepticons for good.
The Dark Energon infusion of the Nemesis works perfectly, bringing the ship to full operational status in minutes. The energy is detected by the Autobots, who immediately set out with Agent Fowler. They arrive to find the 'Con warship already airborne, and it begins firing on them. The Autobots attempt to get close enough to use the Spark Extractor, but the ship hits them one by one with a stasis beam, which a surprised Knock Out notes the ship was not previously equipped with, sending them into stasis lock.
Megatron is pleased at being able to get the Spark Extractor back, but when he orders the ship to move closer, it abruptly changes course, and it is quickly discovered that the Nemesis is ignoring its pilots and flying itself. When Megatron demands the ship's computer be overridden, the Vehicon at the helm is electrocuted. The ship suddenly speaks up with its own voice, announcing it is in charge and on a mission. Knock Out notes its decoding the Iacon database. Furious, Megatron demands they retake control, but when Soundwave attempts to do so, the ship retaliates and he's sent into stasis lock. When Megatron orders the Decepticons to sever all connections to the ship's mainframe, beams of energy sweep through the ship, disabling almost every last one of the 'Cons.
Back at base, Fowler notes that the Nemesis is heading towards North America, with its cloaking field down, no less, and the decision is made to try and contact Megatron to see what's up. On the warship, Knock Out is put into stasis lock while checking on the Iacon data, and Megatron attempts to disable the ship's power core, only to be put in stasis lock as well. When Ratchet contacts the Nemesis, the ship responds and helpfully lets them know its mission is to find the missing Iacon artifacts of Decepticon origin. Ratchet and the humans believe it's the opportune moment to download a copy of the Iacon database, so Fowler and the kids Ground-bridge on board the ship, determining that the ship cannot detect humans, as it left Fowler unmolested while leaving the battle earlier. They find the Project Iacon console, and clambering up Knock Out, plug in the transfer drive Ratchet gave them. Jack notices the ship is heading for Manhattan, the location of the first artifact, and if they don't stop it somehow, the Nemesis will destroy whatever part of the city lies atop the long-buried relic. While trying to change the ship's course, Fowler is electrically shocked into unconsciousness, but the ship, still scanning for Cybertronian-based life forms, is unable to detect the kids.
Though Ratchet wants to bridge the kids back, Jack realizes they have to do something now, and heads to the ship's power core, hoping to de-activate the Nemesis' intelligence by dumping the dark energon out of the fuel supply. There they find the frozen Megatron, and Jack discovers that the manually-operated fuel injection valve is locked in place by Megatron's frozen hand. While he's still trying, the ship finally detects Miko and Raf, assuming them to be vermin that are infesting it. As a manipulator arm starts chasing them, they hide among the energon cubes, but the arm moves the containers aside, eventually exposing them. Jack manages to attract its attention and trick it into hitting Megatron. The Decepticon leader topples over, dragging the lever down and reversing the energon flow. Though the ship tries to use the manipulator arm to move the lever back, it's not fast enough to do so before its intelligence is lost. As the ship "shifts into neutral", the stasis locked Transformers inexplicably begin recovering, and the kids make all haste back through the corridors. While Miko and Raf help a still-loopy Fowler through the Ground Bridge, Jack goes after the transfer drive, but he's still struggling with it as Knock Out comes back online. Jack's saved from an untimely end when Ratchet appears through the Ground Bridge and clobbers Knock Out, taking Jack and the transfer drive with him, just in time to miss the arrival of Megatron, who is rather unhappy with Knock Out. Ratchet gives the now-recovered Optimus the good news about the data they retrieved, but they realize they must act quickly, as Megatron has no more scruples than his ship about harming human life, and the Nemesis is even now bearing down on Manhattan...
Main Article: Flying Mind Gallery
"And when the Insecticons backed off, I got inspired by my proximity to the power core, and did what I do best."
"You trashed Megatron's ride like a rock star in a hotel room."
- -Bulkhead and Miko discussing Bulkhead's victory.
"If the ship isn't cloaked, maybe the communications relays are open and-"
"Ehp, eph, are you suggesting that we just call Megatron and ask him what's happening up there?!
- -Ratchet questions Jack's logic, while all the other humans shrug, "Why not?"
"Doc Knock is knocked out!"
- —Miko makes the joke we've all been waiting to hear.
"On your feet, soldier!"
"...and beavers and ducks and walnuts and Grandma..."
- —Miko helping a debilitated Fowler.
"I'm here to offer a second opinion!"
- —Seeing Knock Out's attempt to operate on Jack, Ratchet gives him the hint that he might want to consider going back to medical school.
- The Insecticons joining the Decepticons, Bulkhead's damage to the Nemesis power core and the ship's crash all took place in the previous episode.
- Megatron makes note of Optimus's increasing ruthlessness and how he would no longer waste a chance to strike, likely referring to his near-termination by Optimus in "Crossfire".
- The Decepticons found their Dark Energon supply back in "One Shall Rise, Part 1", but it hasn't seen much use since the Unicron revelation.
- Soundwave has been trying to decrypt the Iacon database since Optimus Prime recovered his memory in "Orion Pax, Part 3", and has apparently made very little progress.
- Though the Nemesis is established in Transformers: Exiles to be a stasis-locked Trypticon, its identity is left unstated here, as it does not refer to itself by name. Bob Skir has stated it was not meant to be Trypticon waking up. Confusing matters further, the Transformers: The Art of Prime book shows that a unique Trypticon wire-frame CGI design was created for this episode, which (barely) appears in the episode itself on the ship's monitors while the children are on board.
- The Autobots attempt to use the spark extractor, which they acquired in "Operation Bumblebee, Part 1".
- This is the first time Knock Out has used his drill weapon since his premiere episode.
- The Nemesis is stated in Fall of Cybertron to be Trypticon locked into stasis. Megatron's statement that he had failed him and the fact that he had no qualms about condemning Trypticon to eternal ship mode is the reason for Trypticon sending him into stasis in this episode. This is also technically Trypticon's first TV appearance alive since War For Cybertron.
- The Nemesis's voice is listed only as "Warship" in this episode's credits.
- It seems the amount of power required to stasis lock a Transformer isn't enough to kill a human, as the ship was unaware carbon-based life forms were aboard when Fowler was electrocuted, and was presumably trying the same trick it used on Soundwave.
- The Nemesis cryptically hangs up when Ratchet asks why it's gathering the relics, though this was never brought up again.
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