Prime returns to life in this hour special. Two scientists, Jessica Morgan and Gregory Swofford, are in outer space testing a new heat resistant metal alloy. They come upon a spaceship containing the lifeless body of Optimus Prime. Swofford has come to intensely hate all Transformers after being wounded and physically scarred from being caught in the crossfire of a past Transformer battle. Jessica, able to distinguish between Autobots and Decepticons, recognizes Optimus and decides to retrieve the body. The scientists escape with Optimus' body just before a nearby star goes supernova. The explosion causes their own spaceship to be covered with strange cosmic spores. After returning to earth, Dr. Swofford and Jessica's father, Dr. Morgan, discover that the spores infect living things by touch with a crazed Hate Plague (which is believed to be the cause for the countless conflicts that the Autobots and Decepticons have had over so many centuries). Meanwhile, the Decepticons learn of the scientists' new metal alloy and decide to steal it. Galvatron sends the Terrorcons to attack the scientists' lab. Autobot Technobots come to the defense and a fierce battle takes place. The Terrorcons manage to escape with the alloy and the lab is destroyed, leaving Jessica paralyzed. The Autobots take Jessica to the hospital and help her walk again through mechanical aid. Dr. Morgan is dismayed at the violence and at the supposed robotization of his daughter, and states his hatred of Transformers. Swofford and Morgan hatch a plan to use Optimus' body as bait to lure Transformers to the lab and infect them with the hate spores, so that the robots may destroy each other. Jessica is pressured by her father to lure Autobots to the lab, but she tells Rodimus Prime of the real plot. Rodimus is deeply disturbed by the mistreatment of Optimus' body and leads a team of Autobots to recover Optimus. Despite the Autobots' precaution, they walk straight into Swofford and Morgan's trap, and most of the Autobots are either infected or shot and severely injured by infected teammates. An infected Ultra Magnus goes after Rodimus in particular. Decepticons also arrive after finding out about the existence of Optimus' body and suffer the same result. Rodimus and Jessica barely escape with Optimus and bring him back to base. Since Quintessons were the original creators of the Transformers, Rodimus orders Sky Lynx to capture one in order to revive Optimus. Soon after, infected Autobots arrive at headquarters and Rodimus himself gets infected by Wreck-Gar. The hate spores begin to rapidly infect every living thing across earth and beyond. Out in space, Sky Lynx finds a Quintesson on the run from infected Sharkticons. The helpless Quintesson agrees to be airlifted to safety provided that he resurrect Optimus. Arriving on earth, the Quintesson goes to work. After extensive rebuilding, the Quintesson finally finishes. In a glow of light, Optimus Prime rises, declaring that "no force in the universe can stop me". Optimus Prime has been revived through the skills of a captured Quintesson. He is told of the awful situation happening everywhere due to the cosmic hate spores. Optimus expresses his gratitude to Jessica Morgan, then puts the grumbling reluctant Quintesson to work on restoring a whole group of Autobots badly injured from being shot by infected Transformers. The damaged Autobots are repaired, including Bumblebee, who is reconstructed as Goldbug. Optimus feels that the Autobot Matrix of Leadership may offer information on how to fight the Hate Plague, but Rodimus Prime has the Matrix since he is the current Autobot leader and he is also infected. Jessica tells the Autobots that the metal alloy she and Swofford were testing offered resistance to the spores. Getting coated with the alloy will provide Optimus protection in going after Rodimus. Unfortunately, the Decepticons have possession of the alloy. The Autobots and Jessica travel to the planet Chaar where they find Galvatron being hunted down by infected Decepticons. Galvatron is shocked to see Optimus alive. Optimus insists that they must cooperate to fight the common threat. With nowhere to hide, Galvatron agrees. Optimus, being all too familiar with his old enemy's untrustworthiness, only tells him vaguely about the need of the metal alloy in combating the Hate Plague. In order to get to the hiding place of the alloy and with infected Decepticons in pursuit, Galvatron leads the Autobots through a gauntlet of booby traps. The Autobots make it through successfully, much to the sarcastic thinly disguised displeasure of Galvatron. Goldbug and Blaster fall victim to the Hate Plague, but the rest of the party finally obtains the alloy. Jessica accidentally lets slip the precise role of the alloy in the Autobots' plan and Galvatron immediately turns on the Autobots. Infected Decepticons arrive and infect Jessica, who then infects Galvatron. The remaining Autobots escape. Back on Earth, Optimus is coated white with the metal alloy, making him immune from the hate spores. He locates Rodimus and attempts to talk sense into him, but Rodimus is completely mad. The two of them fight it out, with Rodimus trying to kill Optimus and Optimus trying to get the Matrix without hurting Rodimus too badly. Eventually Rodimus gets knocked out and Optimus gets hold of the Matrix. Optimus returns to Autobot base and "enters" the Matrix to gain information from old Autobots who are now One with the Matrix, including Alpha Trion. Optimus travels far enough back to an ancient predecessor who tells him that there is no single being wise enough to figure out a cure. Optimus hypothesizes that if no single being has the wisdom, then maybe the accumulated wisdom over time inside the Matrix could be the answer. In the meantime, infected Transformers arrive at the Autobot headquarters. The captured Quintesson attempts to hold them off unsuccessfully. Just as Galvatron is about to blast Optimus, Optimus exits the Matrix and opens it up, asking it to "light our darkest hour", and thus unleashing all of its power and wisdom. The power of the Matrix spreads everywhere and cures the Hate Plague. During this last sequence of events, the song "You Got The Touch" from the The Transformers: The Movie is played while all of this is happening. Doctors Swofford and Morgan, who started the whole mess, understand the error of their thinking and profoundly apologize. Galvatron expresses his respect for Optimus and decides to have a short temporary truce. Because the Matrix has been completely drained, Optimus tells the Autobots that it is up to all of them to replenish the Matrix with accumulated knowledge and wisdom once again. After this, Optimus orders the Autobots to transform and roll out (just like the way he used to do in the first two seasons of the series). The transformers ride out into the sunset while the song "You Got The Touch" is played in the background again. Followed by transformers: rebirth.