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Optimus gets infected with an ancient virus, and Megatron is the only one who can save him.
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Ratchet has briefly reported he has found the Decepticons' ship, having stumbled upon it by experimenting with various frequency wavelengths, concluding that their electromagnetic shielding is under repair. Also, on the same frequency, Ratchet has found an Autobot emergency beacon. Optimus Prime decides that the Decepticons can wait, as they may have fellow Autobots in danger. He and Ratchet find an Autobot ship that crash-landed into Jasper, Nevada. They climb in, finding dead Autobots infected by a plague in liquid form. A few drops of the plague liquid leaking from a dead Autobot body hanging from the top of the Autobot ship splash onto Optimus Prime.
Optimus is infected with the plague, with visual proof of his right eye infected. Ratchet however did not catch the plague, and identifies it as Cybonic Plague, which according to Arcee, killed off millions of Cybertronians during the war on Cybertron, developed by Megatron himself, Ratchet added. Worse, there is no known cure. Jack suggests that perhaps Megatron wouldn't just create a disease without a cure in case he ever caught it by accident. Bulkhead points out that they can't ask Megatron, having presumed him dead in the Space Bridge explosion. However Ratchet figures that the cure may be in the Decepticon database. He then ground bridges Bumblebee and Arcee into the Decepticon ship.
Arcee goes into the Decepticon computer system, but she cannot find the source for the cure, concluding that the Decepticons do not know the cure either. Bumblebee finds the offline body of Megatron, hooked up to life support. then Arcee automatically plans on extinguishing Megatron, but is halted when Ratchet. Arcee demands one good reason quickly. Ratchet states that Megatron may be Optimus' only hope for survival and asks if the Decepticon leader displays brainwave activity, to which Arcee confirms. He says this is an excellent opportunity and tells the team that they need to enter Megatron's brain via cortical psychic patch, which the Nemesis laboratory has the necessary equipment to perform, to find the cure. Arcee becomes opposed to the idea, asking Ratchet if he even performed the procedure. Ratchet admits he didn't, though he did thoroughly study the theoretical and illegal procedure developed by Decepticon scientists. Arcee suggests bringing Megatron back to base but Ratchet states they have no time. He declares that will not allow Optimus to pass knowing that Megatron will outlive him. Bumblebee volunteers to undertake this dangerous mission. The Autobots then connect the patch cable to Megatron and hide in an alcove to connect Bumblebee.
Bumblebee finds (as translated by Raf) a remodel of the Decepticon capital Kaon, and finds Megatron's mental soul quickly extinguishing a visual representation of Optimus Prime who claims Megatron shall never win. Megatron's mental soul tries to cut Bumblebee, but realizes that his strikes cannot touch the real Bumblebee as he is not a visual representation in Megatron's mind.
After blasting away visual representations of Optimus, Bulkhead, and another Bumblebee, Megatron comes to realize the real Bumblebee is connected to his mind by cortical psychic patch. Ratchet worries that Megatron is becoming self-aware. Megatron then asks Bumblebee (who he refers to as "Scout") what has become of him in reality, then remembers by seeing through Bumblebee's eye the space bridge explosion.
Meanwhile, Starscream berates the Vehicons for not getting the electromagnetic shielding repaired, knowing that the Autobots may be able to find them. Knockout then approaches, reporting that though Megaton's body is "scrap metal", his mind is still functioning. Starscream advises that he keep that to himself, knowing that Soundwave may be eavesdropping. Knockout suggests that he could convince Soundwave that terminating Megatron is the best option, provided that Starscream elevate him to the rank of second-in command. Overhearing their attempts to convince Soundwave, Ratchet fears that if Megatron is pulled off life support, then Bumblebee will be forever separated from his body. Their ploy nears works, until Soundwave spots the chords of the cortical psychic patch.
Bumblebee claims that Optimus is unwell, but Megatron doesn't care, content with blasting illusions of his nemesis. Bumblebee points out that if the plague takes Optimus, Megatron will never get the chance to terminate Prime himself. Realizing that Bumblebee is right, Megatron shows a hologram of the formula for the plague cure. However, he refuses to relinquish it until he finds a way out of his coma. Unknown to the Decepticon leader, Ratchet was viewing everything through the comlink and rewinds the footage displaying the formula and orders Arcee to disconnect Bumblebee immediately.
Megatron sees the visual representation of Kaon disintegrating, then realizes he's been tricked. Megatron pleads Bumblebee to take him as well back to reality. Bumblebee quickly gains back consciousness as Ratchet opens the groundbridge for both Arcee and Bumblebee.
Starscream finds this out, and Arcee blasts the repair chords connecting to Megatron before fleeing into the ground bridge as well. Starscream pretends to be ashamed for this outcome but Soundwave disagrees. Thus, Starscream is forced to order Knockout to keep Megatron on life support. However, the funny thing is that though his vitals are strong, there is no brainwave activity in Megatron's mind
Optimus is cured of the plague and Bumblebee is thanked for what he did, but inside his mind Megatron's soul is there.
- Megatron's question, "So tell me scout, do I still function?" is similar to his line, "Wait! I still function!" from Transformers: The Movie.
- The part where Starscream tells Knock Out if he scratches his back he scratches his is a reference to "Speed Metal" about Knock Out's pain job being scratched twice.
- The actual Kaon appears in "Orion Pax, Part 3", which is where Victor Sigma is located. However it is a different section of Kaon than the image of the section of Kaon in Megatron's mind.
- There are no transformations in this episode.
- When Arcee disconnected the cortical psychic patch, the visual representation of Kaon should not have been disintegrating, only Bumblebee should have.
- Ratchet mentions the redundant quantum allecal rhythm; the compound word's definition is not known, but it could be a method that Ratchet suggested Arcee use while checking the Decepticons' computer system.