The Vok unleash a monstrous weapon, an artificial moon, intending to destroy Earth and all Maximals and Predacons on it. Using a stasis pod equipped with transwarp cells, Optimus flies to the moon to destroy it, but Megatron deviously seals the pod shut, causing Optimus to be destroyed along with the moon.

Optimus, Rattrap, and Airazor discover an alien structure. Meanwhile, Blackarachnia discovers Tarantulas' escape plans and forces him to let her tag along.

Inferno finds a second Golden Disc, marked with alien runes. Megatron and Optimus supposedly agree to a truce, and Tarantulas is determined to get off Earth.

After accidentally killing a feline friend in a fight with Inferno, Tigatron feels guilty and almost leaves the Maximals. But Dinobot and Optimus are able to bring him back. Meanwhile Inferno, Waspinator, and Terrorsaur are looking for a gift to give to the "Queen", with Tigatron and Dinobot at the top of their list.

Tarantulas infects Rhinox with a cold-like virus which causes him to expel his Energon supplies in the form of destructive hiccoughs. Eventually, he will not only destroy the Axalon, but himself as well. Dinobot and Rattrap must cooperate for once as they search for Tarantulas' lab, hoping he has the counter-virus.

Waspinator is possessed by the spark of Starscream.

Scorponok and Waspinator blow up a pit of Energon while Cheetor, Rattrap, Rhinox, and Dinobot are mining in it. All four Maximals are blinded, and must somehow make it back to the Axalon.

The Predacons steal the Energon shielding system from the Axalon. The Maximals are forced to stay in beast mode, and the instincts of their animal counterparts begin to take over.

Tarantulas and Blackarachnia attempt to make a third spider Predacon using a crashed stasis pod, but end up creating Inferno, an insane fire ant Predacon.

The Maximals and Predacons battle for control of the floating island. But Blackarachnia gets it, and plans to use it for her own agenda.

A strange floating island appears. Tigatron and Airazor are soon stranded on it, while Blackarachnia and Scorponok attempt to take control of it.

Rhinox and Cheetor must defend a crashed stasis pod from the Predacons. They are successful and Airazor is born. The concept of sparks is introduced in this episode, it is a concept that is used in Transformer lore that is still used today.

Megatron uses a non-transforming clone of Dinobot to try to shut down Sentinel, while Terrorsaur traps the real Dinobot in a cave.

Rhinox is converted into a Predacon by one of Tarantulas' machines, but his new-found temper becomes dangerous to Megatron and his crew.

Terrorsaur leads a rebellion against Megatron, and the ensuing fight accidentally blows up the Darksyde when an Energon sample is hit. Thinking they have won the Beast Wars, the Maximals decide to salvage parts from the Predacon ship and go back to Cybertron. But the destruction of the Predacons turns out to be an elaborate ruse planned by the Predacons themselves.

The Maximals detect a Cybertronian probe, and try to contact it.

Scorponok tries to infect Optimus with a virus meant to change him into a coward, but it changes the gorilla into a battle-hungry maniac instead.

Rattrap and Dinobot accidentally activate Sentinel, the Axalon's new defense system, before it has learned that the Maximals are friends. Feeling guilty for starting it, Rattrap stays inside the Axalon to shut down Sentinel. Meanwhile, Blackarachnia leads a Predacon mission, trying to break into the Axalon, leaving Tigatron the only one to stop them.

Another stasis pod lands and Tarantulas gets there first, releasing Blackarachnia. Rattrap's loyalty to the Maximals is questioned by Optimus and he nearly joins the Predacons.

A stasis pod lands and the Maximals and Predacons race to reach the protoform. Tigatron comes out, joining the Maximals, but he prefers to stay out in the wild rather than the base, so he asks the Maximals to call him when they need him.

Terrorsaur finds a floating mountain rich with Energon. It makes him incredibly powerful, and he plans to overthrow Megatron and defeat the Maximals once and for all.

An alien probe appears, and Optimus is seemingly disintegrated, leaving the Maximals bickering over who is in command.

The Maximals try to place a Predacon detection system during an Energon storm and Cheetor somehow ends up in the Darksyde, while Terrorsaur ends up in the Axalon. Using Terrorsaur to discover how the transportation occurred, Dinobot goes to Optimus with a plan to beam a bomb to the Predacon base. Meanwhile Cheetor discovers an Energon vein running between both bases.

After losing a prototype comm-link developed by Rhinox, Cheetor tries to redeem himself by sneaking into the Predacons' base. However, Tarantulas captures Cheetor, leaving it up to Rattrap to rescue him.

After the Predacons interfere with Optimus and Dinobot's duel, Dinobot agrees to serve under the Maximals, but the Predacons find an Energon-infested mountain. The two teams have a battle to get the Energon, but the Energon explodes after Dinobot saves Optimus from Megatron. Knowing that the Predacons are not gone for good, the Maximals prepare themselves for the expected long-term conflict for control of the planet's Energon, which Optimus declares to call the Beast Wars.

After travelling into the distant past via a transwarp drive, the Maximals battle the Predacons in outer space, but both ships crash land on a mysterious planet. They scan for beast forms to protect their robot forms from the planet's large amount of Energon. Enraged by the apparent failure to land on Earth, Dinobot challenges Megatron for leadership of the Predacons, but is blown away by Scorponok. After the first battle on the planet between the Maximals and Predacons, Dinobot reappears to challenge Optimus Primal for leadership of the Maximals.