The Return of Optimus Prime, Part 2

Restored to life, Optimus Prime uses the power of the Matrix to cleanse the hate-plague and end the crisis.

Within Autobot City, Optimus Prime has been fully restored to life by Sky Lynx and a Quintesson survivor of the rampant Hate Plague that's infecting the universe. Prime demands to know what has happened during his time on the other side. Sky Lynx recaps the events that had conspired to bring him back, including Jessica Morgan's valiant play to save him from total destruction, the discovery of the Hate Plague spores, and the trap laid out by Jessica's father and her partner Gregory Swofford to infect the Autobots with the spores in revenge, which ultimately spiraled out of control. It was thought by Rodimus, before his infection, that Prime would know what it would take to stop the plague. Prime asks who is available, and learns of the Autobots injured battling Superion.

The survivors are brought back to Autobot City, where the Quintesson manages to reactivate them, completely rebuilding Bumblebee into Goldbug. When Goldbug asks what the plan is, Prime admits that he doesn't have a plan. Without the accumulated wisdom within the Matrix of Leadership (which now resides in Rodimus), he doesn't have a clue as to where to start. That is, until Jessica comes forward with the experimental alloy that she, her father, and Gregory had worked on, which proved strong enough to block the spores. Theoretically, coating Optimus with this alloy would protect himself from the spores' infection and allow him to get close enough to Rodimus to extract the Matrix from him. However, all remaining alloy samples were stolen by the Decepticons. The Autobots decide to retrieve the metal.

Meanwhile, on Chaar, Galvatron is pinned down by his own mutinously diseased soldiers, unable to fight back against their maddening ferocity... until Optimus and his team arrive to save the day, convincing Galvatron that it would be in his best interest to join in an alliance with them. As is his way, however, the Decepticon leader is suspicious of Optimus's motives, especially when he learns they need the alloy he stole, but cannot get a reason for it out of them. He agrees to join in and leads Optimus and his gang down a series of boobytrapped tunnels, their numbers dwindling from the tunnel's natural hazards and the infected Decepticon mob behind them, until only Optimus, Galvatron, Sky Lynx, and Jessica arrive at the alloy's hiding place. Unfortunately, Jessie accidentally lets slip their plan to coat Optimus with the metal after confirming there would be enough of it to do the job, prompting Galvatron to turn on Optimus in hopes of using the process on himself, but he is soon subdued by Sky Lynx. Under coercion, Galvatron loads the alloy onto Prime's trailer but doesn't notice that an infected Cyclonus has managed to sneak in, infecting Jessica in the process. Jessica, in turn, infects Galvatron, forcing Sky Lynx and Optimus to flee back to Earth.

Once on Earth, Optimus is coated with the alloy, and sets out to find Rodimus. He finds him taking down infected Transformers with reckless glee, and attempts to reason with him, which fails. Unwilling to hurt his successor, Prime lures Rodimus to a nearby auto shop, attempting to peacefully subdue and talk Rodimus into helping him, but the Hate Plague is overriding any effort to do so, forcing Optimus to knock Rodimus out and take the Matrix back by force.

Back at Autobot City, Optimus dives into the Matrix to question the elders of the past in reverse chronological order (of their history) to try and find out any information on the spores. The spirit of Alpha Trion warns him that if he travels too far, he risks becoming lost within the Matrix itself. During Prime's journey, the Quintesson that revived him notices a troop of infected Transformers attempting to get in, and manages to temporarily shut them out, giving Optimus the time he needs to finally find his answer. He learns that, in a period of pre-Cybertronian history, the Plague has visited the planet before, but was contained and sealed inside the star Jessica and Gregory found it in using sheer wisdom, though even back then, no one had the wisdom to destroy the spores, and now that it has spread so much throughout the galaxy, it's doubtful that anyone has the wisdom to even contain them again. Optimus then realizes that a source of raw wisdom may be available to destroy the infection once and for all: the accumulated wisdom within the Matrix of Leadership.

The infected Transformers finally break into the base, and corner the Quintesson, who begs them to stop. Galvatron grabs a metal pole, intending to impale Prime. However, Prime's chest opens to reveal a glowing Matrix, surprising the Transformers. Asking it to "light our darkest hour", Optimus Prime releases the energy of the Matrix of Leadership, which spreads across the world and across the universe, and totally eradicates the Plague.

Some while later, in Autobot City, a remorseful Gregory and Jessica's father offer deep apologies to the Autobots, while Galvatron, in a rare moment of calm, shakes his old enemy's hand, proclaiming that Prime has earned his respect and that "there will be no war today." Rodimus (now once more Hot Rod, without the Matrix within him) notes that the Matrix is now empty, its wisdom supposedly lost in order to stop the plague. Optimus, however, disagrees; they have all become a little wiser, now, and although the Matrix is indeed empty of wisdom, it is up to them from then on to fill it again with their knowledge and experience. Optimus, once again the Autobot leader, orders his troops to "Transform and roll out".

—Goldbug and Optimus Prime, the latter of whom is not exactly inspiring confidence

—Optimus Prime, getting back into the swing of things.

—Galvatron fighting his infected and insane troops. The irony fairy just had a coronary.

—Galvatron is no longer so impressive to Cyclonus and Predaking

—Galvatron and Optimus Prime resuming their same old song and dance