Optimus and the Autobots are defending the docked Ark from Decepticon forces. Realizing they have broken through Grimlock's post, Optimus tries to contact him to no avail. Jazz and Cliffjumper are sent to investigate, and whilst eliminating enemy tanks Optimus' turret suddenly deactivates. As he leaves to repair it the room transforms around him, leading him to a brightly lit chamber where he activates the city-sized Transformer, Metroplex. The gargantuan robot disables two Decepticon cannons, being shot point-blank by a third. Optimus is captured soon after by Starscream and his Combaticons and brought before Megatron. As Megatron is about to execute Optimus, Metroplex arrives and pummels him into the ground. Having lost Megatron, Starscream claims leadership of the Decepticons and orders a retreat.
Meanwhile, Jazz and Cliffjumper arrive at the Sea of Rust to locate Grimlock and his Lightning Strike Coalition Force. They stumble upon an enormous tower firing a bright beam into Cybertron's orbit. They find Shockwave at the scene and soon realize it is a Space Bridge. Shockwave escapes the ensuing confrontation, and Cliffjumper becomes trapped, leaving Jazz to fight off the incoming Insecticons. Cliffjumper overloads the tower, and it begins to melt down. Sideswipe arrives to save Cliffjumper and Jazz from the Tower's explosion, and all report back to Optimus.
After the Autobots salvage all the Energon they can from the tower, Starscream and his Combaticons arrive to reclaim it. Onslaught, the team's leader, briefs them on a complicated plan to ambush an Autobot Transport. Combaticons Vortex and Blast Off fly into the canyons and meet Brawl at a bridge the transport must cross. There they destroy the bridge supports. Meanwhile, Swindle engages Autobot ground forces and destroys the wheel struts underneath the transport. The transport transforms to levitate off the ground and engages the Decepticon team. Starscream orders the Combaticons to abort the mission, but they defy him and then combine to form Bruticus, who brings the transport down. Starscream arrives at the crash site and arrests the Combaticons for insubordination.
Elsewhere, Soundwave assembles a newer, more powerful chassis for Megatron. He awakens, frees the Combaticons, and stops Starscream's coronation as King of the Decepticons. He then leads a full scale assault on Iacon, where the massive Decepticon Trypticon's remains are kept. Megatron invades the facility and takes Trypticon's power core. He informs the lifeless beast that he is not to be rescued, but will instead be reassembled into Megatron's flagship, the Nemesis.
Starscream, having been humiliated at the hands of Megatron, infiltrates Shockwave's base where he stumbles upon Grimlock being held prisoner. He offers Grimlock freedom in exchange for his fealty, but Grimlock rejects and throws Starscream aside, escaping. He searches for his fellow teammates, finding Swoop, Slug, and Snarl and defeating the defending Insecticons. Grimlock learns from Shockwave that theirprocessors were tampered with, leaving Grimlock with a speech impairment. Shockwave also found a new planet by way of his Space Bridge inhabited by large creatures; these were used to inspire all of their new alternate forms. Grimlock was further tampered with, as now he cannot transform on command, but instead must be in a state of rage to do so. Grimlock remembers a name that Sharpshot gave them, the Dinobots, and claims it as their new team name. Grimlock then notices another Space Bridge tower that Shockwave has constructed nearby. Grimlock fights his way to Shockwave, knocking him from the tower and destroying it. The crumbling tower falls and the portal in Cybertron's orbit begins to decay.
Before the launch, Metroplex transfers all of his Energon to the Ark and sacrifices himself in the process. Optimus then calls for the launch of the Ark to try and make it through the portal before it closes, but Decepticons arrive in the Nemesis to stop him. Soundwave leads the first wave of troops onto the ship through giant cables and destroys the Ark's automated defense system. Jetfire is then launched into space to disengage the cables. Bruticus launches from the Nemesis and destroys the Ark's fuel line before being blasted off the ship into empty space by Jazz and Jetfire. Nearby Megatron and Optimus engage in battle. Before a winner can be declared, Optimus and Megatron are pulled off of the hull of the Ark and pulled with both ships into the portal, where it finally closes to leave their home planet alone and quiet.
