The Ark returns to Cybertron, with the Autobots aboard reporting no apparent Decepticon activity. Meanwhile, on Cybertron itself, Chromia and another Autobot, Perceptor, break out of their captivity to try to warn their comrades of the Decepticons' passing trap. Unfortunately, they are recaptured with Chromia being forced to watch as Shockwave destroys the Ark with his latest invention, the laser snare.

The Decepticons revel in their apparent victory until the Autobots reveal themselves, with Optimus having earlier suspected their trap and ordered the evacuation of the ship's crew. A large-scale battle occurs between both sides with Prowl taking a fatal shot from Shadow Striker meant for Optimus while Shockwave and Megatron initiate a secret plan.

As the battle continues, Bumblebee, Hot Rod and Cheetor head off to the Well of the AllSpark while Hot Rod deals with Drift, who reveals he faked his defection to the Autobots. Meanwhile, Wheeljack sends Vector Sigma into Unspace and Windblade engages Bludgeon in a final duel that ends with her sending the Decepticon into Unspace as well.

At the Well of the AllSpark, Bumblebee and Cheetor engage Shockwave and defeat him. However, as the AllSpark is placed back into its well, Shockwave sends his spark into the AllSpark to corrupt it and subsequently dies. In response to Shockwave's action, Cheetor sends his own spark into the artifact to reverse its corruption and fully revitalise Cybertron, sacrificing himself in the process. Optimus sends Megatron flying into a swarm of Scraplets, achieving complete victory for the Autobots and ending the war.

Both Autobots and Decepticons are stuck in a never-ending parade loop. Hot Rod, who was not caught in the loop, and Clobber, who was rescued from it by the former, attempt to hack into it to free their fellow Cybertronians. The attempt fails and both are chased by mysterious tentacled troopers with Clobber getting recaptured and needing Hot Rod's help twice. The two later lure in a squad of the tentacled troopers before crushing them under the debris of a derelict building. They later join Perceptor who reveals that the loop the other Cybertronians were currently experiencing is slowly draining them of their sparks. With that in mind, Hot Rod resolves to free everyone from the loop and end the invasion on their home planet.

Clobber, hacking into the loop again, tries to warn some Cybertronians to snap out of the loop to no avail. However, another Decepticon, Dead End, breaks out of it. Exploring the actual room and that his fellow Decepticons were also caught in the loop, Dead End is forced to flee when he accidentally alerts the invaders, the Quintessons. Finding Clobber and Hot Rod at one of Shockwave's old labs, he attacks the latter, having assumed that the Autobots were responsible for bringing the Quintessons to Cybertron. Even though Hot Rod explains everything (also mentioning how he evaded capture and that he found Perceptor who freed himself from the loop much earlier), Dead End remains unconvinced until the Quintessons and their troops, the Prosecutors, find the three Cybertronians and chase them. It is only when the trio hide out at Maccadam's bar that they are able to shake off their pursuers.

Hot Rod hacks into the loop again in a bid to free Optimus Prime from it. Despite his efforts, he is unable to free the Autobot leader, especially when his actions are met with resistance from those enjoying the parade loop. Hot Rod is eventually caught by the Quintessons but is rescued by Clobber, who noticed Hot Rod's absence from Maccadam's bar, and Whirl, who managed to break out of the loop while Hot Rod tried to rescue Optimus. Meanwhile, Perceptor examines Maccadam's bar to find out why the Quintessons did not attack them when they entered in and discovers that it is actually part of a Titan which they had been hiding in the whole time.

Perceptor explains his discovery but Hot Rod states that the Titan, named Iaconus, is not active and thus unable to help them. As he, Clobber, Dead End and Whirl venture deep into Iaconus to obtain a cloaking device that shielded them from the Quintessons, the four end up in a training simulator. Perceptor meets up with the four Cybertronians again, having an arm decapitated and discovered the inner workings of Iaconus as well. The group is then attacked by a crocodile bot which they fend off. As the five approach the cloaking device, Maccadam arrives and discourages them from taking the device before explaining the history of Iaconus. Back at the surface, Hot Rod later decides to awaken Iaconus to stop the Quintessons.

While Perceptor concludes that only a Cityspeaker can awaken Iaconus, Hot Rod leads a team to free more of their comrades from the Quintessons' parade loop. However, the Quintessons discover Hot Rod's resistance team, capturing Hot Rod in the process. Meanwhile, Whirl inadvertently frees Soundwave from the loop when he dislodges the machinery attached to him though Soundwave is currently in poor health. Hot Rod, in the meantime, is brought in front of a Quintesson Judge who explains that they travel to different universes to judge if they are worthy. The Judge deems Hot Rod guilty but Hot Rod escapes with Whirl coming to his rescue, after which, Hot Rod thanks Whirl who is then "thanked" by Soundwave.

Despite working together, both Autobots and Decepticons still do not get along with each other. Soundwave and Hot Rod argue over who should lead the Cybertronian resistance, though Soundwave still freezes up every now and then, a result of being forcefully pulled out of the loop. Even when their team heads out to combat a Quintesson squad, Hot Rod and Soundwave still have different ideas on how to lead. During the fight, Soundwave freezes again, causing the resistance to come to his rescue, during which, they also bring in a Sharkticon working for the Quintessons as their bailiff. Hot Rod later interrogates the Sharkticon bailiff who makes mention of a scientist. Hot Rod asks him where they can find that Scientist.

Hot Rod and Soundwave venture back to the room where the other Cybertronians are kept to confront the Quintesson Scientist. The Scientist ignores Hot Rod's threats, explaining that he was making duplicates of Soundwave from each universe. When the real Soundwave freezes up again, the Scientist fixes him, only for that Soundwave to shoot him upon being fully repaired. Hot Rod and the real Soundwave then try to free everyone from the loop only to be confronted by multiple duplicates of the Scientist. In response, Soundwave sends one of his cassette minions, Laserbeak, to help the other Cybertronians to break in and free all Autobots and Decepticons from the loop. Unfortunately, the Quintessons' tower and ship combine and generate a forcefield...

The Autobots and Decepticons team up in a last-ditch effort to save the universe from the Quintessons.

The Autobots and Decepticons discover the terrible secret behind the Quintesson menace.

Starscream, using his new Quintesson powers gained from his encounter with them, incapacitates the Transformers, thwarting any escape plans they set in motion. While he judges some Transformers, Optimus, Bumblebee and an injured Wheeljack escape into the multiverse. Meanwhile, Windblade heads to Maccadam's, fights off the Quintesson Sharkticons and fully awakens Iaconus with assistance from Maccadam. In response, Starscream summons a brainwashed Croaton to attack Iaconus.

Amidst the battle, Maccadam frees the captives before gettinghuged by a stray blast from Croaton. Starscream then uses Unspace to decapitate Iaconus' head and sends Croaton to destroy Iacon city. Optimus, Bumblebee and Wheeljack return from the multiverse and confront the Quintesson Scientist, with Wheeljack locating the Scientist's real body and hugging it before Starscream attacks Optimus's team.

As Starscream prepares tohug all Transformers, Megatron returns from the multiverse with Dead End, the newly recruited Insecticons and a Decepticon shuttle named Astrotrain to assist everyone using his newly gained multiversal powers. Windblade frees Croaton from the Quintessons' control, but the strain of the task fragments her consciousness which scatters all across Cybertron.

Megatron reveals to Optimus that he obtained another Matrix of Leadership from the multiverse. Using the combined power of their Matrixes, Optimus and Megatron destroy Starscream for good. Following the battle, Megatron orders a ceasefire and that the Decepticons and Autobots will possess one half of Cybertron each.

In an attempt to locate a missing Windblade, Bumblebee goes on a spying mission in Decepticon territory.

In their search for Windblade, Bumblebee and Chromia discover secrets hidden within the legendary Crystal City.

A forgotten Autobot returns to Cybertron, searching for revenge.

To help Windblade, Bumblebee finds he must travel to Cybertron's forbidden moon.

The search for Windblade continues as Grimlock joins Bumblebee on a journey to prehistoric Cybertron.

A rescue mission to save Jetfire reveals a secret Decepticon operation.

Bumblebee and Chromia's search for Windblade takes them into Cybertron's gaseous Argon Sea.

Optimus Prime leads a strike team of Autobots on a mission deep into Decepticon territory to destroy a dangerous artifact.

In the series finale, the Autobots and Decepticons face the Other One, a powerful version of Megatron from an alternate universe.