A year after assuming leadership of the Autobots, Rodimus Prime hosts an intergalactic sporting event, which falls victim to an attack, resulting in the abduction of Spike Witwicky, Kup, and Ultra Magnus. Rodimus is quick to blame the Decepticons, who are divided and weakened by the loss of their leader, Galvatron. But Galvatron's fellow reformatted Decepticons, Scourge and Cyclonus, may have found a way to restore their leader to power. The real culprit may be a new face, but one with a link to the histories of both Autobot and Decepticon, manipulating both sides to take their own revenge.

Rodimus Prime devises a plan to rescue Ultra Magnus, Kup, and Spike from the Quintessons, even as he attempts to probe their connection to the Autobots' past. Meanwhile, the Decepticons revive Galvatron and restore him to full strength.

After escaping Quintessa, the Autobots are stranded the interstellar garbage dump, Goo 8739B. As they attempt to find a way off world, the Quintessons forge an uneasy alliance with the Decepticons.

Rodimus Prime goes on a "vision quest" inside the Matrix to learn the Quintessons' true role in the Transformers' origins. Meanwhile, Galvatron plans a two-pronged attack on Cybertron and Earth with his newest creation: Trypticon.

Titans clash as the Autobots and Decepticons battle for control of Cybertron, while Trypticon and Metroplex duel on Earth. And in the shadows, the Quintessons prepare their sinister endgame that will destroy them all.

A Quintesson scientist kidnaps Ultra Magnus, Wreck-Gar, Cyclonus, and Captain Faireborn for a series of twisted experiments. But greater concerns arise when the scientist's ship is damaged in an ion storm, causing it to drift helplessly through space.

In his younger days, Kup experienced his greatest personal failure when he encountered the alien monster known as Chaos. The beast's unique crystals are the deadliest element in the galaxy, attracting the attention of Galvatron, who plans to use them against the Autobots. When a human space station is destroyed, Kup is sent spiraling irrevocably toward a second confrontation with Chaos.

The several Autobots seek shelter to make repairs to their ship and find a Mausoleum they built for their causalities. They discover that Optimus Prime is no longer in his tomb, they find him alive, trying to build an escape shuttle. Rodimus happily hands the matrix back to Optimus, but their former leader is not himself. Soon they'll discover who brought Optimus back and why.

After being exiled from the Decepticons, Octane has become a smuggler. While being hunted by the Sweeps, he inadvertently awakens the "ghost" of Starscream, who possesses Cyclonus and starts plotting his revenge.

While the Autobots believe him destroyed by Metroplex, Trypticon secretly regains his strength in the Socialist Democratic Federated Republic of Carbomya. With the help of the renegade triple-changer Octane the Decepticon duo glut themselves on super-energon refined from Carbomyan oil, prolonging their stay by appeasing the African nation's ruler Abdul Fakadi with an ongoing supply of stolen monuments from around the world. Galvatron and the Decepticons discover Trypticon's location and attempt to take over Carbomya outright, but the Autobots come to the rescue with the aid of the mighty Metroplex.

The Autobots find an asteroid where Quintessons have made a time window back to the rebellion on Cybertron. The window is damaged in battle and several Autobots are trapped in the past while Alpha Trion is brought into the present.

Daniel and Wheelie want to throw Ultra Magnus a surprise birthday party, but his creation date is unknown. They go in search of a missing storage asteroid containing Autobot archives, but are captured by Scourge and Cyclonus.

Daniel and Grimlock fall through an old Quintesson portal into another world. They meet a red wizard who seeks to use Grimlock against the forces of his enemy the Golden One. The Autobots learn of their absence and send in a rescue team.

The Decepticons discover a world where the people speak in music. Galvatron wants to find three of them so that their combined harmony can used to destroy Autobots.

Weakened from battle, Cyclonus and Scourge escape through a mysterious space anomaly. After crashing on a planet, they are nursed to health by the pacifist robotic inhabitants, and take over their world.

Cyclonus is concerned about Galvatron's mental and emotional state and takes him to planet where he can get treatment.

In an effort to get his body back, Starscream's ghost possesses Scourge and makes a deal with Unicron to perform three tasks.

The Quintesson trick the Decepticons into unleashing an underground trans-organic creature developed on Cybertron in the years before the Transformers.

The Quintessons create a device that makes Daniel's nightmares attack both Autobots and Decepticons.

First Aid quits the Autobots over his pacifism. This becomes a problem when Trypticon attacks a malfunctioning Metroplex.

The alien worlds Xetaxxis and Lanarq have been at war for thousands of years, and will destroy each other within a generation unless Rodimus Prime can convince their leaders to sue for peace. The Quintessons have been manipulating the conflict for personal gain, and have misplaced a journal that incriminates them. The Autobots must retrieve the journal before the peace talks break down, but the Decepticons are also seeking to acquire it.

The Quintessons invade the planet Junkion and use subliminal messaging tactics to convince the Junkions to be efficient and tidy...and that all other races are their enemies. When the transmitter sending out the messages is damaged in a battle between the Autobots and Decepticons, the Junkions decide to send their message across the galaxy, leading to warfare erupting on numerous planets...

Criminals get help from a mysterious person called "Snake." He has a device which transfers the personalities of Rodimus, Springer, and Arcee into human bodies. The criminals take the transformers bodies on a crime spree. The human Autobots must find a way to get their bodies back. Watch for a surprising twist for the masked person known as "Snake."

While fighting the Decepticons, Grimlock bites some controls. The feedback boosts Grimlock's intelligence. When many of the Autobots are captured. Grimlock builds the Technobots, and makes a sacrifice so that his new creations will be better suited to fight the Terrorcons.

Captain Marissa Faireborn and the Technobots run afoul of a smuggler named Dirk Manus who is working with the Quintessons.

Autobots and Decepticons with animal modes are summoned to battle an energy being named Tornedron.

Rodimus is having problems with all the responsibilities that come with being a leader. He is attacked by decepticons who manage to take the matrix from him, transforming him back into Hot Rod. The Autobots want to go after the decepticons right away to get the matrix back. But Hot Rod isn't as anxious. Scourge tries to give the matrix to Galvatron, but it doesn't work for him, Scourge uses the matrix on himself, and becomes more powerful, and attacks Galvatron, and then goes on a rampage. Hot Rod witnesses a sensei training a student, and learns a valuable lesson, and realizes what he has to do.

A clash with Autobots forces Quintessons to flee. A Quadrant Lock is the Quintessons' only possibly refuge, but things go very wrong. The Autobots and the Quintessons find themselves unable to exit the Quadrant Lock the way they entered, and they aren't alone. It turns out that the entire planet Zimojin has spent thousands of years there because of the Quintessons. Naturally, the Zimojins still hold quite a grudge. The key to escape for all ultimately lies in Perceptor, but Katsudan inadvertently gives him trouble first.

A group of scientists find the body of Optimus Prime, and some spores that bring out aggressive tendencies with whomever makes contact with it. The scientists have a grudge against the Autobots, and use Optimus's body to lure them into a trap. As the spores spread through the Autobots and Decepticons, Rodimus orders Sky Lynx to find a Quintesson in a desperate attempt to bring Optimus Prime back to life.

The spores have spread across the Galaxy. Optimus hopes to find a cure in the Matrix, which is inside Rodimus Prime, but Rodimus has been infected by the spores. Optimus must find a way to get the matrix, without becoming infected.