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Transformers: Deviations is a one-shot comic story from IDW Publishing, part of their Deviations mini-series of "What if" storylines. It explores an alternate version of the events of The Transformers: The Movie in which Optimus Prime didn't die due to injuries sustained at the hands of Megatron.
As the Battle of Autobot City unfolds, a narrator discusses Quantum theory as Optimus Prime faces off with Megatron, and the purpose of this exposition is revealed as Hot Rod is tackled by Kup, preventing him from interfering in the duel as in the film. As a result, Megatron is unable to use him as a living shield from Optimus' attack, and after he picks up the discarded blaster and attacks the Prime, Optimus delivers a fatal shot. Optimus then leads the Autobots in driving the remaining Decepticons from the city, while Starscream recovers Megatron's cannon as proof of his demise. After ordering the remaining Decepticons aboard Astrotrain, he shows off his prize before claiming leadership of the Decepticons; when the wounded Thundercracker, Skywarp, and Insecticons are then dumped en route to Cybertron, the absence of Megatron leads to their being devoured by Unicron.
The Autobots gather the bodies of their fallen comrades, and Optimus announces his intent to press the fight against the Decepticons. Hot Rod is skeptical of the need, but Ultra Magnus then notes that the Decepticons will presumably have a new leader quickly, and then berates the young Autobot for his presumption in both this matter and his attempt to interfere in Optimus' battle. Optimus breaks up their fight and reminds them of their fallen friends, while a glow from within his chest causes Hot Rod to speak of the fallen joining the Matrix of Leadership. The Autobots then board a pair of shuttles, and Optimus surprises his subordinates by assigning Hot Rod to Magnus' shuttle to watch over Daniel Witwicky. Magnus expresses his doubts about Hot Rod's competence, but Optimus-apparently seeing something of his younger self in the young Autobot-believes that a capable mentor like Magnus can help Hot Rod reach his full potential.
Meanwhile, back on Cybertron, Starscream is crowned leader of the Decepticons, only for Unicron to arrive in orbit; at Soundwave's insistence, Starscream goes to greet the new arrival. Unicron then demands that Starscream hunt down Optimus and destroy the Matrix of Leadership, and Starscream agrees in exchange for an upgrade. Now known as Megascream, he leads his Seekers in an attack on the Autobot shuttles after Hot Rod mentions to Daniel that he's been experiencing visions of Optimus' death. Against both Ultra Magnus and Perceptor's recommendations, Hot Rod initiates a hard reverse of the engines in his shuttle after Magnus is wounde, causing them to burn out and send the shuttle careening towards Junkion. Alerted that Unicron has devoured Moon Base 1, Megascream flies back to Cybertron to confront his "master," who soon sets his sights on Cybertron itself.
Forced to set down on Quintessa for repairs, Optimus and his crew-consisting of Kup and the Dinobots-run afoul of the Sharkticons, whom they fight off before breaching the "court" of the Quintessons. Noting that the hostile aliens recognize them but unaware why, the Autobots focus on freeing the Quintessons' former prisoners, including Kranix of Lithone, who briefs the Autobots about the threat of Unicron before joining them. Meanwhile, the damage to Magnus' shuttle leads to it crash-landing on Junkion; Hot Rod and Daniel manage to escape, but Magnus, Perceptor, Springer, and Arcee perish in the resulting explosion. Hot Rod blames himself for the tragedy but is comforted by Daniel, and the pair are then rescued by the arriving Optimus, who similarly encourages the young Autobot after Hot Rod confesses his error. The group then travels to Moon Base 2, where they regroup with the other Autobots as Unicron attacks their home planet.
Believing the Matrix to be the key to Unicron's defeat, Optimus resolves to face the monstrous Transformer alone, and departs in a shuttle unaware of a stowaway aboard. Landing on Unicron, he is confronted by Megascream, who demands that he turn over the Matrix before combining with Soundwave, Astrotrain, Dirge, and Ramjet to form an even more massive version of himself thanks to Unicron's upgrades. He then blasts Optimus and grabs the wounded Autobot leader, only for Hot Rod to intervene and rescue the Autobot commander. Taking the Matrix from Optimus' broken chest due to sensing its connection to him, he then plants a teleportation disc on Optimus to send him back to the moon base. Megascream attacks the young Autobot, but he manages to open the Matrix, unleashing an explosion of energy that consumes the mismatched opponents and Unicron himself.
Shortly thereafter, Optimus and the other Autobots reclaim Cybertron, hopeful that the Great War has ended and that a new era of peace awaits. Optimus then looks into the sky and sees a vision of two fallen heroes: Alpha Trion and Hot Rod, the latter of whom he acknowledges as Rodimus Prime.