1: The Arrival - Optimus Primal, Cheetor, Rattrap, and Blackarachnia find themselves on Cybertron with no memory of how they got there, stuck in their organic beast mode forms, infected with a virus that prevents them from transforming, causes them intense shocks, and pursued by transforming tank drones. They are led underground to a supercomputer called The Oracle, which cures them of the virus after giving Primal a cryptic message "The seeds of the future lie buried in the past. To unleash the warrior within, you must tame the beast without. Seek the balance, Optimus Primal. Transform your destiny. Transform and transcend". However, they still can't seem to transform. After being attacked by motorcycle drones, Primal manages to transform and drives them off. On being able to transform, Primal simply says "I understand." Above on the planet surface, Megatron learns of the Maximal's survival.
2: Master of the House – Primal tells the others that The Oracle wants them to transform only when they have to, not taking their beast modes for granted or wanting to escape them (Cheetor rightfully asks "Haven't we learned this lesson already?"). Primal tells him it is a very different situation now. He, Cheetor and Blackarachnia manage to transform. Rattrap is having a difficult time (Because of his narcissistic view of the situation). Cheetor and Blackarachnia decide to investigate the planet surface, emerging to find that the whole planet is deserted except for themselves and the drones that attack them. Primal insists on seeing if the Maximal Elders in the Council Citadel can help. Once inside, he is greeted by Megatron, now encased in a suit of control armor. Megatron claims that he won the Beast Wars and now rules a Cybertron rebuilt into his own image, of purely technological purity, devoid of organic life. The drones, Vehicons, sparkless transformers who serve his will, populate the planet. However, the ingenuity of the Maximals defeat the mindless Vehicons. Frustrated, Megatron loses control and transforms to his dragon beast mode, deactivating the drone in the process. After fighting, Megatron reconnects to his harness and summons drone to attack Primal, forcing the Maximals to retreat. Primal tells them that this is all his fault for not destroying Megatron.
3: Fires of the Past – After being attacked by drones, Blackarachnia dreams of Silverbolt (Who she doesn't remember). Megatron, meanwhile, is assured by his Diagnostic drone that all elements of his beast mode have been wiped from his body. However, when the Maximals conquer the drones, Megatron transforms again and angrily yells at the drone "You call this cured?" At which the drone mentions that the Maximals have 'free will'. Megatron then summons three sparks from a chamber of them below him (the sparks of the missing population of Cybertron). Meanwhile, Blackarachnia decides to sneak to the Central Spaceport, followed by Rattrap. They are then encountered by three drones, with sparks: An aero jet called Jetstorm, a motorcycle called Thrust, and a tank called Tankor. After escaping, they infiltrate the building and find the Autobot shuttle they had flown from Earth was shot down by the planet's defenses, stranding all six of them on the planet. Rattrap is confused by the notion that there were six of them. Blackarachnia goes off to find the ship, while Rattrap heads back, having had enough. By happy accident, Rattrap discovers that the generals can't scan them in beast mode. Having found the ship, Blackarachnia discovers images of them all in their Earth bodies, plus Rhinox and Silverbolt. The generals arrive and blow up the shuttle. Primal is furious that their only chance of finding answers was destroyed.
4: Mercenary Pursuits – Irritated that the three generals can't destroy the Maximals, Megatron tells them that he will reward them if they bring back the Maximals. Jetstorm and Thrust fight amongst themselves while Tankor actually finds the Maximals. After a long fight, Tankor stands victorious and brings the Maximals to Megatron. Eventually, they break free and Primal tries to convince Tankor to come with them. He blows open the door, allowing them to escape. However, Megatron erases Tankor's recent memories. Primal later on admits that he sensed something 'familiar' about Tankor.
5: Invasion – The Maximals discover archive footage of how the planet got infected with the virus, the overtaking of the planet by Megatron, and the arrival of the drones. Blackarachnia finally decides to tell Optimus about Rhinox and Silverbolt being out there somewhere.
6: New Regime – As Optimus goes into deep meditation to find answers through the Oracle, Cheetor takes charge and Rattrap finally manages to transform out of concern to help the others.
7: Discovery – During a battle, Thrust saves Blackarachnia multiple times. She imagines seeing flashes of Silverbolt every time this happens, leading her to believe that Thrust has Silverbolt's spark. They find a spark extracting machine which must've been what Megatron used to steal all the Cybertronian's sparks. Thrust saves her again, then flees once the other Maximals arrive. After Blackarachnia tells them that Thrust's spark was a Maximal, they realize that the same must be true for Tankor and Jetstorm.
8: Descent – Cheetor, Rattrap, and Blackarachnia debate which Vehicon to revert first. Cheetor suggests Tankor because of his dim-wittedness, making him the easiest to subdue. Blackarachnia argues about Thrust, but Cheetor puts her down. She goes to distract Thrust and Jetstorm while Cheetor and Rattrap attempt to capture Tankor. Rattrap uses an interface device to plug into Tankor's memories. He sees the other Maximals headed back to Cybertron through his own eyes, apparently getting back his own memories of how they got back. He sees how Megatron escaped and vanished into a transwarp hole, causing the shuttle to buck due to the difference in the time rift. Then the ship is shot down by Cybertron's defenses. After crash-landing he sees Primal, Cheetor and Blackarachnia hit with the virus and reverting back to their original bodies. Rattrap then whacks Tankor's head, telling him to "stop giving me my memories and give me yours!" When he plugs back in, he sees Silverbolt and himself being hit with the virus. Then a tank drone looms down on him, and in the reflection of the tank drone, he sees whose eyes he is looking out of: Rhinox.
9: Revelations – Cheetor is skeptical that Tankor is really Rhinox, due to the difference of their intellect. Tankor then wakes up and after briefly seeming to recognize them, he attacks them. After pinning them, Tankor convulses when Cheetor begs Rhinox to listen to them. On another plane, Primal encounters Rhinox, who is in as much pain as Tankor. Primal offers to help him, but Rhinox says that this is all Primal's fault and that Megatron's view is right "As long as sparks remain individualistic, the wars will only continue!" Primal withdraws from the Matrix in anguish. Meanwhile, Blackarachnia saves Cheetor from Tankor, but is stopped from attacking him when Cheetor insists that he's Rhinox. After offering again to help him, Rhinox replies that he doesn't need their help. He reveals that he's been conscious inside Tankor, unable to communicate, only watch and learn. Cheetor is relieved that he will be able to help them defeat Megatron. Rhinox, who sounds corrupted, says Megatron is the planet's only hope for technological perfection. Cheetor calls Rhinox an imposter. Rattrap questions whether Rhinox's very spark may have been affected by Megatron's control due to forcing Rhinox's consciousness out from within Tankor. Cheetor tells Blackarachnia to 'fix' Rhinox. Before they can, Primal arrives, solemnly telling them that if they tampered with his mind any more, they were no better than Megatron. Even if Rhinox was corrupted by Megatron, if The Oracle willed Rhinox to become good again, he would do so on his own. Rhinox departs, telling Primal that they are now enemies.
10: Reborn – Megatron is enraged that he can't get rid of his beast mode. His Diagnostic drone suggests removing his spark and placing it in a purely robotic body. Megatron, not wanting his spark vulnerable, declines. He sends Thrust, Jetstorm, and Tankor (Rhinox) along with the drone, to capture a Maximal to reverse their beast mode scanned into a technological form for Megatron. They attempt to capture a Maximal, but they escape. Jetstorm and Thrust give chase, leaving Tankor behind with the drone. Tankor reveals his changed personality to the drone, saying that he is a combination of Rhinox and the original Tankor, resulting in something greater. He reveals that he feels Megatron's goal has merit, but that he should rule Cybertron instead. Later, after the Maximals have escaped the other Vehicons, the re-programmed Diagnostic drone (who now only appears loyal to Megatron to spy on him) contacts Tankor, who has found the Oracle.
11: The Key – Tankor believes that the Oracle is in fact the super computer Vector Sigma, which gave all transformers life. His interest, however, is finding the Key to Vector Sigma, which has the ability to turn organic material into metal. Tankor tries and fails to enter the Oracle, not being a 'receptive spark' like Optimus Primal. Tankor then throws the drone (who has no spark at all) inside, where it uncovers the Key. Meanwhile, the Maximals are still trying to figure out exactly what they are supposed to be doing to stop Megatron. Rattrap is still mad at Optimus for not letting them cure Rhinox, thinking the 'if the Oracle wishes him good, he will do so' view Primal has is complete garbage. Cheetor also expresses concern that Optimus may have too much faith in the Oracle. They are interrupted by Tankor, who tries to use the Key of Vector Sigma on them. But the power seems to be too much for him, causing him to overload and shut down. After Tankor is led away, Megatron inquires as to how Tankor deactivated. Cheetor demands respect from Optimus since he led the Maximals during Primal's extended time with the Oracle. Primal shoots back that the group doesn't need two leaders. Later, Tankor is revealed to be alive, having faked his death.
12: The Catalyst – The Maximals hold a funeral for Rhinox, which Tankor is spying on. Meanwhile, the drone tells Megatron about the discovery of the Key to Vector Sigma, suggesting duplicating it and using it to purge Cybertron of all organic elements. Megatron asks what the effect on his own beast mode would be. The drone assures him that it will finally be gone, but (as Tankor reveals) will drive him mad until he is offline forever. Megatron demands the Key be fitted to his drones to test on the Maximals. Not what Tankor had intended. Blackarachnia, meanwhile, has made a device to overload reprogramming effects on transformers (in secret) in order to turn Thrust back into Silverbolt, then (hopefully) Tankor into the real Rhinox. While the Diagnostic drone has Jetstorm and Thrust wandering Cybertron aimlessly to distract them, Blackarachnia swipes Thrust into a cyber-web and implants the device on him, reverting him back into – Waspinator. Waspinator explains that he choose to return to Cybertron out of boredom, but thanks to flashbacks, we find that he was actually kidnapped by a time-jumping Megatron when he escaped the Maximal's capture. Regardless of how he got there, Waspinator is happy to be a "cool biker-bot", not getting blown up as often, and that "chick-bots dig brooding, loner bit". Blackarachnia is a little more than disappointed at this revelation, but then Jetstorm bursts in and accidentally is implanted with a device as well, causing him to revert into Silverbolt instead. He and Waspinator then argue over Blackarachnia until Jetstorm and Thrust's drones arrive with Keys in their cannons. The devices on Waspinator and Silverbolt are shot off and they promptly return to their Vehicon personalities. Blackarachnia escapes. Optimus believes that the Oracle has been tampered with, due to some problems communicating with it. The drone, meanwhile, has convinced Megatron to download the Key to Vector Sigma into all the tank drones.
13: End of the Line – Tankor tries to order the tank drones, but finds he can't. He'll need Megatron to command them for him. Optimus then receives a fake message from the drone through the Oracle, guiding him to the Plasma Energy Chamber, which can overload any electrical-mechanical systems. Cheetor tries to sway Optimus away from unleashing the Plasma Energy Chamber. Tankor is pleased that Optimus found it, knowing he would never use it, and also that Megatron could never take that chance. Megatron is disturbed when he finds out from the drone that Optimus found the chamber. The drone suggests deploying the Key before Optimus has a chance to use the Plasma Energy Chamber on him. Megatron knows that Optimus wouldn't stoop that low to defeat him and, after the drone somewhat lets it slip that it has ulterior motives to his own, Megatron disables it. Tankor is frustrated and heads out with his own Key. Primal then encounters Megatron, but sees that everything is being reformatted by the Key. He goads Megatron, who transforms to beast mode and the two of them wrestle until Primal is hit by a Key laser, shot by Tankor. Tankor then tries to shoot Megatron as well, but is restrained by energy binders. As Megatron gleefully reveals, the Vehicons are programmed to not hurt him and thanks Tankor for his part in helping Megatron achieve victory. Primal threatens to unleash the Plasma Energy Chamber. Megatron says that Optimus doesn't have "the machine-like clarity to do what is logical and necessary to win". Optimus says "Not this time". Then the chamber activates and starts to destroy everything technological on the planet, including the planet itself.