The Return of Optimus Prime

While testing a new heat- and radiation-resistant alloy in deep space, scientists Jessica Morgan and Gregory Swofford stumble upon an Autobot shuttle about to crash into a nearby star. A cursory evaluation of the shuttle reveals a deactivated Optimus Prime within. Jessica, unable to sit by and watch the Autobots' greatest leader die convinces Gregory to help her rescue him, despite Gregory's own reservations. In a previous accident stemmed by a conflict between Optimus and Megatron, which he blames on Optimus, Gregory's face was scarred, rendering him distrustful of any Transformer from then on. Fortunately, they are able to rescue the Autobot leader and move away from the shuttle as it collides with the star and causes it to nova, their alloy proving sufficient enough to withstand the intense heat and radiation the explosion produced. With both missions a success, they head for home, but not before Gregory notices a series of unusual spores attaching themselves to their ship's hull. Back on Earth, in Washington, D.C. , Gregory and Jessica's father begin running tests on the spores, and soon discover them to be a highly infectious contagion able to induce and exacerbate hatred and destructive impulses in any sentient being they contaminate. Despite the obvious danger, the two scientists are eager to continue studying the spores, a prospect Jessica openly objects to. Before a consensus can be formed, however, their lab is attacked by the Terrorcons, who are after their new alloy. The Technobots quickly join in to protect the humans and the metal, and in the resulting battle, Jessica is severely wounded and taken to the local hospital. This prompts an angry backlash from Jessica's father, who is encouraged by Gregory to get revenge on both factions by reviving Optimus and using him as a carrier for the plague. This is exacerbated when they learn Jessica was rendered paraplegic in the accident, and now needs a specialized exosuit to walk. Unfortunately for them, they are unable to revive Optimus, and are content to scrap his body to make more of their alloy. Jessica makes a futile attempt to save Optimus by appealing to her father's and Gregory's sense of morality, and is only successful when they realize that, as the Autobots' leader, they could use Optimus' body as bait to lure the rest of the Autobots into a trap. Because of her friendship with the Autobots, Jessica is forced to lure them into the fate something she hates and hopes she will not learn to hate her father and colleague for. She arrives on scene with Ultra Magnus, and meets with the new leader, Rodimus Prime. She tells Rodimus it's a trap though he does not care and assembles an assault team to retrieve Optimus' body so he can rest in peace. Ratbat hears this and goes back to an abandoned football stadium where Soundwave plays the recorded conversation for Galvatron, who is planning to destroy Prime's body. Then he took off with Cyclonus, Scourge, the Sweeps, the Stunticons, the Combaticons and the Predacons, leaving Soundwave and Ratbat in the football stadium. When they get there, Rodimus tells Defensor and a few other Autobots to stay behind, while the rest retrieve Optimus, but warns them not to touch any red dust. Rodimus tells Ultra Magnus to take the Aerialbots and Throttlebots and retrieve Optimus' body, while Rodimus and Jessica distract Swofford and Morgan. Defensor and several Autbots stay behind to guard against the Decpticons. Rodimus and Jessica find the body of Optimus in the wrong room, and realize too late the trap that is being laid for the other Autobots. Gregory floods the lab containing Ultra Magnus, the Aerialbots and the Throttlebots with the red spores; infecting all of them. Morgan and Swofford's plan is successful as the spores make Ultra Magnus, the Aerialbots and Throttlebots go crazy and fight each other and quickly the Decepticons (except Galvatron) join the diseased army. Rodimus and Jessica escape from being infected and head back to headquarters to Wreck Gar, not knowing that Ultra Magnus is following. Defensor is seen clearing the bridge while the sickened Superion comes on scene and infects Defensor. Kup, Blurr, Wheelie, Steeljaw, and Bumblebee try to subdue Superion but become severely injured. Rodimus asks Wreck-Gar and the Junkions if they can revive Optimus but they are unsuccessful. Rodimus shuts down Metroplex so he cannot be infected and tells Sky Lynx to retrieve a Quintesson to revive him. The sickened Ultra Magnus appears and chases Rodimus to an alley. It seems like he's doomed only to be saved by Wreck Gar with his lasso, but unfortunately Wreck Gar gets infected, and quickly infects Rodimus. The spores travel throughout the galaxy pitting everyone against each other, human and Transformer alike. In space, Sky Lynx manages to find a Quintesson getting chased by a group of diseased Sharkticons. Sky Lynx says he will save the Quintesson, in exchange of reviving Optimus which he agrees. After a bit trouble, the duo revives Optimus, who awakens as the entire universe is descending into madness.

The episode begins with a revived Optimus thanking the Quintesson for bringing him back to life. Optimus then asks what happened and who is left. Sky Lynx informs him that the Autobots that escaped infection are in need of repairs by the Quintesson. Soon the uninfected are restored, but Bumblebee was too injured to be restored to himself and had to be rebuilt into a new body. Optimus gives him his new name: Goldbug. Optimus informs them that without the Matrix, all is lost and since it's inside Rodimus, he will need the heat resistant alloy. They set off leaving the Quintesson, Wheelie and Steeljaw at Metroplex. On Chaar, Galvatron is fighting his crazed minions and the Autobots save him. Galvatron then guides them to the alloy. Galvatron agrees to show them the room with the alloy. However, they find the way perilous. They make it in by avoiding a giant spider, energy sucking leeches and Galvatron's crazed minions. During the trip, Optimus' last wave of Autobots are infected by the crazed Transformers leaving only him, Galvatron, Jessica and Sky Lynx. After finding and loading the alloy, Cyclonus secretly infects Jessica who in turn infects Galvatron as he realizes why Optimus wants the alloy. Now everyone on Chaar is infected but Optimus and Sky Lynx who are forced to flee the planet leaving behind friends and foes alike. Back at Metroplex, they coat Optimus with the alloy, as they discover where Rodimus is. Sky Lynx drops Optimus off at a junkyard, where Rodimus is racing with the other infected Transformers. Optimus battles him for the Matrix but is nearly killed until the intervention of Sky Lynx in the battle, with the unfortunate result of Rodimus infecting Sky Lynx. Optimus knocks Rodimus unconscious on a conveyor belt, and retrieves the Matrix. At Metroplex, Optimus goes into the Matrix to seek a cure. Meanwhile, the crazed Transformers arrive as the Quintesson closes the door behind them to protect Optimus. Optimus finds the essence of Alpha Trion within the Matrix and he asks for the cure but Trion does not know it, so Optimus travels further back into the knowledge of the Matrix. An early Autobot leader reveals that they had encountered the spores, but could not find a cure. One of their old wise men was able to contain the spores and he injected himself into the sun - the same sun that these spores came out of. Optimus then realizes that wisdom is the cure and awakens just in time to use the wisdom of the Matrix to wipe out the plague, making everyone safe and sane again. In the aftermath, both Dr. Swofford and Dr. Morgan apologize for their actions, realizing their unfounded hate for the Autobots began a pandemic of hate. Galvatron, in a rare moment of calm, walked towards Optimus which allowed him to refuse the scientists' apology and shaked his hand. Galvatron told Optimus that there will be no war today and has earned his respect. Also, in a surprising show of admiration, Galvatron orders a cease-fire (at least temporarily), his inherent madness apparently also cured by the Matrix's wisdom. Speaking of the Matrix, Rodimus, who becomes Hot Rod again, notes that the wisdom of the ancients is gone; Optimus disagrees, though, noting how they have all grown a little wiser from the experience, and must now fill the Matrix again with all their accumulated knowledge and experience from then on. The restored leader of the Autobots, Optimus orders them to "Transform and roll out (for home)".