Two spaceships, one manned by benevolent Maximals, the other by evil Predacons, crash-land on a pre-humanoid planet while en route to Earth. Their crews assume indigenous animal forms to protect themselves from an overabundance of natural energy, transforming into robots to do battle. Thus, the Beast Wars have begun...
Realizing that without the Maximals she would never have existed, Blackarachnia actives the Ark's defenses and forces Megatron out of the ship. The Maximals start initial repairs and the time storm subsides a bit, but Optimus Prime's life still hangs in the balance - it could swing either way. Megatron rallies his troops to make sure it swings in his favor.
The Maximal Depthcharge flies into a temporal disruption while out searching for Protoform X, and is sent back in time to the Beast Wars. He and Rampage has some unfinished business, and neither cares if anything gets in their way.
Unable to jury-rig defenses using parts from the Ark, the Maximals send Rattrap down under water in a small capsule to retrieve Sentinel from wreckage of the Axalon. But Megatron wants to lay his hands on it too, and Rampage and Depthcharge fighting it out in the area, nobody's safe.
Two young cave-humans are separated from their parents by an attack from Megatron's new transmetal enhanced raptor clones. Optimus chases off the raptors and charges Blackarachnia and Cheetor with escorting the kids back to their homes.
Using a newly discovered blank protoform, and his part of Rampage's spark, Megatron creates a clone of Dinobot incorporating his enhanced transmetal 2 technology. Discovering the experiment, Cheetor and Depthcharge try to destroy the equipment, but it is activated during the fight and blows up - the cat getting caught in the blast.
Afraid of what he's becoming and unable to control it, Cheetor tries to hide his temporary transmetal 2 transformation, leading the others to believe a mutant beast has destroyed him.
Blackarachnia is getting tired of the distrust, and when she overhears Optimus and Rhinox discussing removing her Predacon programming, and the fact that it might leave her mindless, she rushes out on her own... straight into the claws of the waiting Dinobot.
Megatron is building a disruptor ray to scramble the Maximals' circuits, but needs an organic lifeform who won't be affected by it to finish putting the shielding into place. He has one of the cave-human children kidnapped, and it's up to Rattrap and Depthcharge to save her.
Blackarachnia attempts to use the transmetal driver on herself, but all it accomplishes is to disrupt her Predacon programming, making it deteriorate quickly to the point that it will make her mindless unless it is removed.
Optimus is implanted with one of Tarantulas' bugs, this one letting Quickstrike remote control him. After securing the Maximal base, Megatron goes after the original Megatron's spark, hoping it will give him equal power to Optimal Optimus.
The aliens, the Vok, send Tigerhawk to Earth to stop Megatron's meddling with time. He crashes into the Predacon base, but the Predacons have no intention of takeing this lying down... especially Tarantulas.
While Inferno, Quickstrike and Waspinator go looking for a new ""colony"", Megatron discovers one of Tarantulas' secret projects - the reactivation of the gigantic Decepticon warship that shot down the Ark before it crashed into the sea.
Destruction rains down on the Maximals as Megatron unleashes the weapons of the Nemesis. Optimus orders a desperate attempt at getting the Ark airborne.