1: Fallout – Primal descends into the Matrix, witnessing Cybertron destroyed by the Plasma Energy he unleashed, releasing that "Megatron didn't destroy Cybertron. I did!" He is then tormented by visions of the others blaming him. Primal then realizes that he makes his own choices, not the computer. The Oracle acknowledges this fact, but tells him that his fate still lies with him. Rhinox appears, saying that Optimus must fix what he did and that he himself must remain with the Matrix. Primal abruptly returns to Megatron's control room, back to normal. He redirects the Plasma Energy and Key to Vector Sigma energy into the Matrix itself. Everything returns to normal, except the Vehicons are inactive. Cheetor, Rattrap, and Blackarachnia go to the Citadel and witness Megatron, Tankor, and Optimus' deactivated bodies. Plugging into Cybertron's computer, Blackarachnia confirms that the planet is 'brain-dead'. Jetstorm and Thrust show up, proving they didn't go offline. After brief fighting Cheetor calls it off, saying that the war is over. After they leave, the three Maximals head down to the Oracle and find Optimus inside it. He asks that they forgive him for being so careless. Cheetor says that there is nothing to forgive. But Primal disappears back inside the Matrix, seeing the collective sparks of transformers past, present, and future, inviting him to join them. Primal realizes that the reason they were sent to pre-historic Earth during the Beast Wars was to bring back the organic DNA within their beast modes to the planet to help resist Megatron's tyranny. He confirms that he is ready to join the Matrix, but not today. Primal then emerges out of the Oracle and resumes command. Above ground, they find someone else who returned from the Matrix: Rhinox.
2: Frenemies - Primal and the others express relief at Rhinox being back to his old self. But, he isn't. Rhinox is incredibly bitter and tries to avoiding talking to any of them. Primal asks him what is wrong, and Rhinox bursts out "You are! You're the reason I became what I was! You knew my mind was altered by Megatron. You could have saved me from that. But your ridiculous belief that I could become good again if I wanted too left me trapped as Tankor. I had no control over Megatron's programming, how could I? I used to admire your leadership, but now you've let me down. I don't want forgiveness from you, Optimus. I don't want anything from you." Optimus is shocked to hear this, but can't deny it either. Cheetor tells Rhinox that he's not the only one who has given up on someone they looked up too. Rhinox asks indifferently if that was supposed to pull some emotional strings on him. Rattrap sides with Rhinox, telling Optimus that he was adverse to Optimus' theory of Rhinox since he voiced it. Rattrap then tries to bond with Rhinox about their mutual disgust for their leader, but Rhinox rebuffs him too, saying that he doesn't want sympathy from anyone. He just wants Optimus to feel as horrible about what happened to him as possible. They are then attacked by something that looked like a T-Rex with wings (A combination of Megatron's three past beast modes during Beast Wars). After driving it off, Rhinox departs, taking Rattrap and Blackarachnia with him. Cheetor stays behind, saying that his faith in Optimus has never wavered, despite their arguments in the past. Off to the side, a humanoid robot with no evidence of transformation abilities on it, watched them.
3: Two Minds Joined - Megatron's robot form talks to his internal computer in an emotionless, mechanical way, asking what had happened to him. The computer informs him that all of his experiments on purging his beast mode from his body, combined with the Plasma Energy and Key to Vector Sigma energy that was released, resulted in what he had been hoping for- separating the two. Except, his spark was split in two as well, the emotional half remaining in his beast mode(s), and the computerized half staying in his now non-transformable robot body, making the beast version of him feral, and the robot half nothing more than a walking computer. Megatron questions how to rejoin his spark, and the computer says the only way is to re-combine the two halves and bodies. Megatron refuses to take his beast mode back, and decides to use a spark extractor on his beast half, then rejoin it to his robot body. Jetstorm and Thrust have encountered beast-Megatron and start attacking it out of fear. Megatron commands them to lead it to the citadel, where he can remove the other half of his spark. Rhinox, hell-bent on getting revenge on Megatron, goes to the citadel as well, hoping to find him there. Instead, he finds beast-Megatron and the Vehicons. Recognizing the connection, Rhinox goes after Megatron's beast mode(s) and prepares to destroy it. Primal arrives with Cheetor, demanding that Rhinox stand down. Rhinox tells him that he is no longer taking orders from him anymore and that this thing was Megatron, or at least part of him. Primal counters by saying that the thing seems purely organic and not evil at all, insisting that they don't harm helpless living creatures. Meanwhile, robot Megatron has arrived ordering Jetstorm and Thrust to hold down the beast. Primal and Cheetor stand in front of it, swearing to protect it from Megatron. But the beast attacks them from behind, knocking them down. It approaches Megatron willingly. Rhinox is held down by the two Vehicons and watches as Megatron rips out the other half of his spark from the beast mode(s) and implants it back into his robot body. Having accomplished his goal since reaching Cybertron, Megatron reactivates the drones and sends the Maximals running underground. Rhinox angrily confronts Optimus, saying that once again, his stupid belief for goodness in all living things caused Megatron to repair himself and regain control of the planet. Officially declaring rebellion, Rhinox leaves the Maximals. Rattrap goes with him out of loyalty and sympathy for Rhinox and discouragement at Optimus' recent actions. Cheetor asks Blackarachnia if she is going to betray Optimus too. She says she is going with them, but only to try to suede the others to come back. Primal starts to thank Cheetor for sticking with him, but he says "You have made some questionable decisions lately, Big-Bot. I understand why. You've been under a lot of pressure since returning here, being single-handedly in charge of the only hope of stopping Megatron. But, you have to understand that Rhinox does have a very valid point. This belief you have, about goodness in everyone, it has gotten us into a tight corner. We could've stopped Megatron and gotten the old Rhinox back by now if we'd taken the opportunity. This isn't the Beast Wars anymore, Optimus. If something fails, we can't just try again the next day. In this battle, every decision matters." Outside the citadel, the beast mode beast opens its eyes.
4: In Darkest Knight – Rhinox and Rattrap discuss Jetstorm and Thrust, knowing that they, like Rhinox, have sparks of lost transformers that were reprogrammed to serve Megatron powering them. Thinking to gain allies and take away Megatron's support, Rhinox agrees to attempt to change the two Vehicons back into whoever they were. Blackarachnia tells them that Silverbolt is inside Jetstorm and tries to point out that Thrust is Waspinator, but they won't listen to her and head out. After realizing that, like Optimus, Rhinox also has a connection to the Oracle, due to them both being brought back from the Matrix through it, they hope to use that connection to revert Silverbolt back to normal. Optimus and Cheetor, meanwhile, are captured by Megatron and held inside the citadel. Rattrap distracts Thrust while Blackarachnia lures Jetstorm away and Rhinox 'reformats' him. After a painful metamorphosis, Silverbolt returns. He is bitter, however, loathing himself, no longer believing in honor or heroics. Blackarachnia points out that they have to rescue Optimus and Cheetor from Megatron. Silverbolt agrees, but only in order to confront Megatron. Rhinox stays behind. In the citadel, Megatron interrogates Primal and Cheetor for information on the Oracle in order for him to use it to manipulate the sparks he holds captive. When Silverbolt and Blackarachnia arrive, Megatron explains the reason he chose Silverbolt's spark to be one of his generals was because of his sense of honor, which he believed would make him stay loyal to his goals. He and Blackarachnia try to suede Silverbolt to their side. Eventually, Silverbolt attacks Megatron, freeing Primal and Cheetor in the process. Primal has to drag Silverbolt out to stop him from attacking Megatron further due to impending arrival of drones. Once out of the citadel, Rhinox and Rattrap approach the others. Primal welcomes Silverbolt back, but he shoves past Primal. Rhinox tells Silverbolt that he knows how he feels. Silverbolt confronts him, saying that he doesn't. Unlike Rhinox, he actually enjoyed being a villain and being freed from his code of honor. When Rhinox explains everything else that happened, Silverbolt agrees that Optimus seems unfit for leadership anymore and sides with Rhinox. Blackarachnia gives Optimus an 'I'm sorry, I have to stay with him' sort of look, before going with Rhinox, Silverbolt, and Rattrap. Optimus lowers his head in sadness, having lost another friend.
5: Slave – Blackarachnia continues to try to pursue Silverbolt. But he keeps telling her that love is a luxury he cannot afford as long as Megatron is still out there. Optimus is still severely depressed and doubtful about his own leadership skills. Cheetor tells him that during the Beast Wars, he was the best leader they'd ever had. Optimus then says "If that's true, then what's wrong with me now?" Cheetor suspects it has to do with dealing with situations that no leader has ever had to deal with before. Infiltrating the citadel, Rhinox confronts Megatron about his reprogramming. Megatron calmly tells him that Optimus is the one he should be mad at, not him. Rhinox says he is mad at everybody right now, and that destroying Megatron will bring more good and resolution. Besides, he doesn't want Optimus dead, he wants him eternally guilty and to suffer for his decisions. Megatron expresses surprise at how he is still very similar to Tankor, even now. Enraged, Rhinox fires upon him, but Megatron evades his attack and laughs, saying that "Even not under my control, you remain my slave!" Rattrap, Silverbolt, and Blackarachnia drag Rhinox out of the citadel away from Megatron. Rhinox is furious because now he doesn't know what is real to him or what is still left from Megatron's tampering with his mind. Silverbolt expresses interest as to why the Oracle is connected to three of the most differently minded transformers in the universe: The good (Optimus), the bad (Megatron), and the gray-area (Rhinox).
6: A Wolf in the Fold – Silverbolt gets infected with something. Rattrap helps Silverbolt to his feet, asking if he is okay. As Silverbolt says he is undamaged, Rattrap is infected too. They rejoin Rhinox, who sees drones flying all over the place with canisters containing red gas. Just as Rhinox realizes that Megatron must have formed some version of the infamous Hate Plague, Rattrap brushes against him, infecting him too. Optimus and the others join them after witnessing the drones too. Blackarachnia grabs Silverbolt's hand, getting herself infected. Silverbolt promptly pulls his hand away. Cheetor puts his hand on her shoulder to comfort her, but, as such, is infected. Optimus asks Rhinox if he knows what's going on here. Rhinox retaliates angrily. Expecting as much, Optimus shows no concern until everyone else starts bickering as well. Giving up on them, Primal leaves to confront Megatron about the canisters. Megatron sent out the virus to grab his attention, in order to have a small chat, saying that they both want the same thing: harmony. They argue over the merits of free will and chaos, harmony and individuality, until Primal sees that the others are fighting each other, then leaves. Primal arrives on the fighting Maximals, declaring that the fighting is caused by a virus. The others mock and criticize him until Thrust and his drones attack, causing the ground under Rattrap to break open. Cheetor catches Rattrap, and then starts to fall. The same pattern is repeated with Blackarachnia catching Cheetor, Silverbolt catching Blackarachnia, Rhinox catching Silverbolt, and finally, Optimus catching Rhinox and hauling them up and out. Back on the surface, the drones have disappeared. All of them helping each other cured them of the virus. Silverbolt and Blackarachnia reconnect, though Silverbolt is still disgruntled, especially because he caused them all to be infected. Rhinox is moved by the notion that Optimus saving him proved that he did still care about him. He decides to dissolve his rebellion from Optimus and rejoins his command, but their disagreement is by no means solved. Optimus suspects that the virus did not cause the conflicts, only magnified them. He disbelievingly wondered aloud whether Megatron might be right after all.
7: The Strike – After complaining to Megatron that the odds of one versus six are crazy, Megatron says that he is no better than Tankor or Jetstorm. Thrust points out that he's remained loyal and that Megatron's choices caused the other two to turn against him. Megatron then takes out two more sparks from his storage and creates two new Vehicon generals: Obsidian (A twin bladed helicopter) and Strika (A six wheeled ground vehicle). Thrust is impressed with them, but Megatron makes it clear that they rank above him. After pretending to be stupid, Obsidian and Strika successfully trap the Maximals with their batches of drones, Obsidian observing that "Although he took his name from a great leader, Optimus Primal never learned the first rule of warfare: Never underestimate your opponent." Obsidian officially introduces himself and Strika, declaring that by protecting and serving Megatron, they are doing what they've always done: protect and serve Cybertron. Primal realizes that they've been fighting the two greatest generals in Cybertronian history. After the Maximals escape, Obsidian and Strika report to Megatron and await their punishment. Megatron, however, is pleased with their loyalty and thanked them for keeping the Maximals preoccupied, allowing him to finalize his plan for the sparks. Meanwhile, Rhinox pessimistically states that Obsidian and Strika have fought a thousand wars together and won them all. Optimus vows to never let Megatron violate another spark.
8: The Search – Optimus, receiving a vision from the Oracle, realizes that Megatron has moved the sparks of the captured Cybertronians. He sends everybody out in groups to find them. Silverbolt and Blackarachnia enter the inevitable 'stop being like this' discussion they have every episode, Rattrap and Cheetor squabble as usual, while Rhinox and Optimus discuss philosophical differences, all while searching for the sparks. The three groups are attacked by Thrust, Strika, and Obsidian respectively. Optimus encounters a hologram of Optimus Prime, who tells him that the Oracle lies within him, needing only to summon it. Rhinox tries to stop him, but Primal can't hear him and, as Rhinox is attacked by Obsidian, he accesses the Oracle. Prime's hologram becomes Megatron, proving it to be a fake out. Megatron gloats that he sent Optimus the fake vision to separate his troops and allow Optimus to access the Oracle for his benefit. He has already studied and mastered most of the Oracle's secrets, but there were some crucial parts missing . . . until now. Megatron starts downloading the Oracle from Optimus. After completion, Megatron releases Optimus in the middle of Rhinox's battle with Obsidian's drones. Optimus is too stunned to do anything. But then the beast complied of Megatron's beast modes runs up and obliterates Obsidian's drones. Obsidian retreats and the beast runs way. Rhinox confronts Optimus about letting Megatron trick him into accessing the full power of the Oracle. Optimus reveals that he actually let Megatron do it on purpose, to allow Optimus to access information from him at the same time, giving him the location of all the sparks.
9: Sparkwar – In the citadel, Megatron opens up the spark containment grid, allowing a few sparks to float out. Megatron absorbs them into his body, and he grows slightly bigger with each couple of sparks consumed. The generals engage the Maximals to stop them from disrupting Megatron, who is now half the size of Unicron, consuming more sparks. Optimus yells at the sparks to resist Megatron's summons, but they really have no control anymore. After Megatron gloats that since he is one with the Oracle, no power can stop him, Rhinox and Optimus both realize that, since they are connected to the Oracle as well, either of them can stop him somehow. Optimus runs up to engage Megatron, but Rhinox knocks him down, saying "Let me stop you from making another big mistake, Optimus." He fires his chain guns up at Megatron to get his attention. Optimus is pinned down by Obsidian and Strika, while the other Maximals are held up by drones. Thrust engages Rhinox, preventing him from reaching Megatron. Rhinox, in an act of desperation, uses his Oracle connection to reformat Thrust back into Waspinator. Seeing this, Megatron slams a massive fist down to crush the revived, confused and scared Waspinator. Then Megatron's beast mode component beast runs up and knocks Waspinator out of the way of Megatron's hand and is crushed beneath it. Rhinox climbs onto Megatron's hand as he rises it back up into the air, then leaps off to hover before Megatron's giant face, glowing white as he accesses the Oracle within him. Megatron, realizing what Rhinox is about to do, reaches out to crush him, but Rhinox releases everything in him, including his connection to the Oracle, and his own spark, against Megatron, causing all the sparks inside him to be released back into their containment. Rhinox's body evaporates and Megatron returns to normal size and collapses, seemingly deactivated. The Maximals gather and express shock and gratitude for what Rhinox had done. Optimus, still sad that he never technically made up with Rhinox, was nevertheless grateful that he gave up his life to stop Megatron and save the sparks for him, officially redeeming himself for his earlier actions as Tankor. Waspinator, still in shock about what was happening around him, asks where "Horn-Bot" went. Optimus says "He is where he belongs, one with the Matrix." Then he turned quickly and said "Waspinator? When did you . . . what the . . . huh?"
10: Spark of Darkness – The Maximals are surprised and a little annoyed about Waspinator returning, but as Cheetor says "Hey, better him than Thrust, right?" Waspinator is slightly frustrated as well, saying he wants to go back to being Thrust again. Silverbolt says "Well, there are two big problems with that. One, Megatron is dead, and two, even if he wasn't; I don't think he would want Thrust back. Or you, for that matter." Waspinator looks down at Megatron's empty shell, then rejoices happily about not being bossed around anymore and that he can finally lead the Predacons. But his celebrating is cut short by Obsidian and Strika. Primal asks them to join them, since they, like Waspinator, have nowhere else to go. They reluctantly agree, seeing it as their only option. Primal orders everybody to work on moving the recovered sparks into transformer bodies to repopulate Cybertron and complete their mission. During their search, a spark wanders through the streets, inhabiting random deactivated drones to attack the Maximals with. During his encounter with it, Rattrap discovers he needs to re-polarize it to stop it randomly jumping from one body to another. He captures it in a spark extractor, but then it breaks free and enters a Diagnostic drone. The drone rises up and exclaims "I live! I LIVE! I-" then upon realizing what he is, Megatron exclaims "What kind of puny body is this?" He tries and fails to leave the body and bitterly remarks being "Trapped like a rat, by a rat." When the other Maximals arrive, Megatron explains that his spark was not destroyed, merely lost. Waspinator asks Megatron to change him back into Thrust. Megatron says that Waspinator was too much trouble, both as a Predacon and a Vehicon. Obsidian and Strika arrive and, seeing Megatron, they grab him and escape with him. Out of spite to Megatron, and fear that he may be blasted by them otherwise, plus the fact that his beast mode fits more with their group anyway, Waspinator joins the Maximals. Optimus realizes, with massive regret, that Rhinox didn't actually kill Megatron, but only turned him into the monster that he was but no longer is. Megatron criticizes Obsidian and Strika for withdrawing him from battle. Since he has lost the sparks, he declares that "The time for action is now!"
11: The Downward Spiral – Megatron downloads a template of a new body for him to use. Primal announces that the Oracle was aware of Megatron accessing it and allowed it to happen, but he has no idea why. The Maximals have relocated inside the unguarded and abandoned citadel as a base, in order to protect the hostage sparks held there. Megatron orders Obsidian and Strika to attack the Citadel to reclaim the sparks. All Maximals except Optimus, Cheetor, and Rattrap (Who remain inside) try to hold off the assault. Eventually, the shields around the building fail and it is surrounded by drones.
12: Endgame – Optimus receives an Oracle vision that tells him, "You already have the wisdom, along with the strength of your convictions." among other things. When he returns, he has a mysterious spark glow around him, which he gives to the others as well, telling them that they are now ready to face the Vehicon army. Silverbolt and Blackarachnia have a quiet moment together. Waspinator is stunned that the others now officially count him as part of the team. The 'spark-boost' allows them unnatural abilities to take on the legions of drones. Vehcions get into the building regardless, however, and Primal peruses them. Outside, Obsidian and Strika are tricked into getting blown apart by Cheetor and Waspinator. They turn to greet a shadow that they think is Optimus, but turns out to be Megatron, in his new body, who blasts them both. Reaching the spark chamber, Optimus takes down the drones, but then is greeted by Megatron, whose new body is an exact replica of Optimus' previous body from the last stages of the Beast Wars. Outside, Rattrap, Cheetor, Blackarachnia, Silverbolt, and Waspinator's sparks are extracted. Megatron tells Primal that the era of the Maximal has reached its end, and that now "It's your turn."
13: Seeds of the Future – "So, Optimus Primal. It all comes down to you and me. Or, should I say, you and you." "Megatron. In my old body." "Minus the impediment of a beast mode, of course." "But why?" "Victory is most delicious when seasoned with irony, is it not?" Primal declares that Megatron will not get the sparks. But Megatron shows him the sparks of his companions, who he adds to the spark containment chamber. Enraged, Optimus and Megatron start their fiercest duel yet, spanning the whole of Cybertropolis. Megatron finally grabs Optimus and takes him to a throne built into the Council Citadel and opens the spark chamber, absorbing the sparks and preparing to ascend to supplant the Matrix and achieve godhood. As the sparks enter his body, Megatron grows bigger. Primal tries to talk him out of it, saying that each spark is but part of the Matrix and that together, they add to its totality. However, Megatron cannot fully activate the Oracle, as he and Primal are linked. Megatron then severs the link and Optimus fears he has failed. However, the sparks of his comrades speak to him, inspiring him on. Primal tells Megatron that the balance the Oracle had been seeking was the balance of eternal enemies: Megatron and himself (the seeds of the future), buried in the past (Cybertron's core). He then manages to knock Megatron off balance and pushes him down into the core of the planet. As they plummet, Primal says "A great transformation awaits, Megatron. Prepare to achieve . . . your destiny." Upon impact, Megatron and Optimus both die in a flash of bright light. The other Maximals awaken and find that the planet has changed, not in appearance, though. Out of the citadel, the revived Cybertronians rejoice at being freed. Waspinator is happy to win and not get blown apart at the end for a change. Silverbolt, back to his old self, sweeps Blackarachnia off her feet. Rattrap makes a quiet eulogy to Rhinox. While Cheetor gets a vision from the Oracle of Optimus' spark joining the Matrix, telling him to "Transform and Transcend" to which Cheetor replies "I understand." Cheetor then leads the Maximals over to their revived civilization, ready to rebuild and repopulate their home, the wars being over at last.