The vision of Pentius he has just witnessed leaves Megatron disoriented and distracted as the Decepticons' aerial forces bombard the Autobots' command position, but soon, the villains' tactics start working against them. The atmospheric alterations brought on by the acid rain they previously unleashed starts to affect the Decepticons' systems, and they begin dropping out of the sky; once on the ground, they are met in battle by the fighting-mad Autobots—joined at last by Omega Supreme—who have survived their bombardment thanks to Trailbreaker's forcefield. Leaving his men to fight, Megatron makes for Trypticon's fallen body, hoping to transfer Pentius's spark out of the giant before the Quintesson restores him, in order to save Cybertron from being consumed by the beast. Before departing, he gives Soundwave one last order: if he fails, burn Iacon to the ground to spare it that fate.

Elsewhere on the battlefield, Hot Rod comes up against Onslaught, but is saved by his old friend Slinger, who now sees the error he made in joining the Decepticons. No sooner have the two comrades made peace, however, than Slinger is ripped limb from limb in a surprise attack by the Predacons, leaving Hot Rod to face them alone. Fortunately, help soon arrives for the young Autobot: having slain his old foe Blackwall by stabbing him through the head with his firesword, Grimlock rallies his Dynobots and brings them to Hot Rod's aid. Hot Rod and Grimlock take on Razorclaw together, and Grimlock shatters the Predacon leader's jaws by pulling them apart with his bare hands.

Megatron easily fights his way through the Autobot unit at the base of Trypticon, but is given momentary pause when faced with Bumblebee, who can see fear in Megatron's eyes. Though impressed with the little 'bot's courage and perception, Megatron impales him on some debris and carries on his way. Optimus Prime spots his old enemy and heads after him; Motormaster tries to bar his way, but as the two charge each other in vehicle mode, Optimus proves himself King of the Road, barrelling into the Stunticon leader and hurling him aside. Omega Supreme deals with the rest of the Stunticons, preventing them from interfering with Optimus's mission, and the Autobot leader soon catches up to Megatron atop the fallen Trypticon's head. As the pair engage in combat with energy weapons, Megatron cryptically warns Optimus of the threat posed by the Quintessons, and tries to goad the Prime into killing him, seeing it as the only way to destroy Pentius—the essence of whose spark remains fused to his own—before he can revive Trypticon. Realizing what Megatron is trying to force him to do, Optimus offers to help him find a way to destroy the malign presence, but Megatron believes it impossible without his death. Optimus refuses to accept this, and unleashes the power of the Matrix of Leadership; its burning white fire successfully eradicates Pentius, but Megatron expresses no gratitude, vowing instead that he will never stop hating Optimus despite what he has done for him. Optimus, sadly resigned to the fact that the spark of the 'bot he once considered a friend became corrupt long before Pentius influence touched it, knocks the weakened Megatron out with a single punch.

Moments later, Prime addresses the Autobots and Decepticons via a huge hologram broadcast, announcing Megatron's defeat, calling for an end to the fighting and vowing that the Decepticons will face justice. Megatron is subsequently imprisoned, and Optimus's surety in, and dedication to, the Autobot cause is left stronger than ever.

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