Beast Wars: Transformers - Season 3

As the Maximals begin to fade from the time stream, Blackarachnia switches sides and saves Optimus Prime with a life-support machine. The time storm fades, but Prime is still in danger so Optimus Primal takes Prime's spark into his body to stabilize it until Prime's body is repaired. The energy from Prime's spark causes Primal's body to mutate into a new "Optimal Optimus" form. Meanwhile, Rampage destroys the Axalon's supports, causing it to fall into the water below. Optimus later returns his ancestor's spark to his body after the repairs are done. Realizing that Megatron will continue to target the Ark, the Maximals gather what they can salvage from the Axalon's wreckage and begin turning the volcano around the Ark into a new base.

Depth Charge, a Maximal from Colony Omicron, arrives on planet Earth looking for Protoform X, wanting revenge on Rampage for killing his comrades long ago. Depth Charge's frustration alienates him from the other Maximals.

After failing to set up base defenses, the Maximals attempt to salvage Sentinel from the wreckage of the Axalon. Rattrap pilots a submarine into the submerged ship, where he is attacked by Rampage. Depth Charge arrives, but only wishes to kill Rampage. Without Depth Charge's help, Inferno and Waspinator steal Sentinel from the Maximals, and it is installed into the Predacon base.

Megatron sends several prototype Transmetal II cyber-raptors to attack the early humans and the Maximals. Depending on who perfects it first, the new technology has great potential in determining the outcome of the war.

Megatron creates a Transmetal II clone of Dinobot, and Cheetor and Depth Charge attempt to interrupt the process; instead, Cheetor is presumed dead after he is exposed to the machine in an explosion. The Predacons soon come under attack from a mysterious feral beast, as a heavily damaged Cheetor returns to Maximal base.

After returning to base, Cheetor has nightmares and soon transforms into the beast from the previous episode. The other Maximals begin to hunt the creature, unaware that it is Cheetor. Megatron claims ownership of the new Transmetal II Cheetor, and sends Dinobot II to capture him. Cheetor eventually harnesses his new form.

When Blackarachnia overhears Optimus and Rhinox discussing her Predacon reprogramming by Tarantulus, she comes to believe that Optimus has decided to surgically remove Blackarachnia's Predacon core without regard for the risk to her and she deserts the base. While on the run she is hunted by Dinobot II. Silverbolt pursues as well, and confronts her on her desertion, at which point she reveals to him why she left. When she confronts Optimus with this, she is told that while the reprogramming could be beneficial to her, it is and always has been her choice to make whether or not to undergo the process. Feeling that the threat to her life is over, she returns to the Maximals.

Megatron kidnaps a young protohuman, Una, to finish a giant disruptor ray that targets Cybertronians. Una follows her directions from Megatron but Rattrap and Depth Charge arrive and save her when the child destroys the machine unintentionally.

Blackarachnia attempts to become a Transmetal II with the help of the alien device she had stolen. However, thanks to the intervention of Silverbolt, the experiment takes a terrible turn and threatens her life. Rhinox travels into her subconscious to try to rid her of her Predacon makeup, but Tarantulas and the Predacons are successful in destroying Blackarachnia indirectly. However, as Silverbolt is out for revenge, the alien device reincarnates her body into a Transmetal, thus giving her a new form.

During an attack on the Maximal base, Optimus is hit with a burrowing cyberbug that allows Quickstrike to take control of his body. Tarantulas and Quickstrike form an alliance in order to destroy the Ark and Megatron. Tarantulas convinces Megatron to use the spark of the original Megatron to upgrade himself as Optimus did. Once Megatron absorbs his namesake's spark, Tarantulas has Optimus (controlled by Quickstrike) drop Megatron into the lava. Blackarachnia manages to stop Tarantulas, using her past knowledge of his work. After he was thought to have "died", Megatron rises from the lava, having now become a gargantuan red fire-breathing dragon.

Quickstrike is put to trial for his betrayal of Megatron, but it is interrupted when the Vok send Tigerhawk, a supernatural fusion of Tigatron and Airazor, to stop Megatron's interference with time. They do not realize, however, that Megatron has part of his predecessor's spark within him, thus destroying him would cause another timestorm. Upon his arrival, Tigerhawk destroys the Predacon's ship. Tarantulas captures Tigerhawk and proceeds to kill his Vok control. The experiment goes fatally wrong however, and Tarantulas is killed. The sparks of Tigatron and Airazor reunite with the body of Tigerhawk and he is welcomed back home to the Maximals.

With the destruction of the Predacon base, Megatron is forced into a corner once again as the Maximals hunt for him. Megatron sends Inferno, Waspinator, and Quickstrike to find a new base, while he goes with Dinobot and Rampage to search the debris of Tarantulas' lair for anything that may turn the tide for the Predacons. They find an underground passage that leads to a minisub that runs on a submerged track – which in reality leads to the Nemesis – the almighty Decepticon warship piloted by Megatron that first attacked the Ark on the way to Earth. Depth Charge is dispatched to destroy the submerged colossus, but inadvertently kills himself when he destroys Rampage with raw Energon. Rampage's death causes Dinobot to scream in pain. Nevertheless, the Nemesis rises from the ocean, with Megatron at the helm. Meanwhile, Waspinator quits the Beast Wars.

The Nemesis has proven to be powerful and dangerous under the now-insane Megatron, killing both Maximals and Predacons alike. Tigerhawk is destroyed with a large energy cannon, and Inferno and Quickstrike both get killed in Megatron's whimsical attempt at taking out a group of proto-humans. Optimus fights Megatron alone, while Dinobot II decides to aid the Maximals by sending them data about the Ark (a consequence from his spark now being independent, which apparently allows him to think more for himself and like the original Dinobot, though the episode hints that Dinobot II has become a conduit for the memories of the original Dinobot from beyond the grave as he recalls the last words spoken to the original Dinobot from Code of Hero, though this is never outright confirmed. However the clone loses the metallic echo his voice originally possessed upon his creation and begins to show signs of Dinobot's personal code of ethics, citing the concept of honor, which up until that point the clone did not care about, to Megatron when he is about to unleash Nemesis' firepower on a single proto-human after physically stopping him from opening fire on him). The Maximals receive the data and discover an Autobot shuttle in the Ark, which Rhinox flies and crashes into the Nemesis control tower, taking out Megatron as it goes all the way through both sides. Optimus flies away while Dinobot II bids farewell and goes down with the ship. The Nemesis is now out of control and flies off toward South America, where it would be discovered during the Great War. The Autobot shuttle and the Transformers on board are safe to resume their original place in time. The Maximals return to Cybertron triumphant with Megatron as their prisoner.

In a deleted scene, Optimus rips the original Megatron's spark from Megatron's chest and restores it within its rightful body.

Meanwhile, Waspinator, who quit the Beast Wars last episode, is shown to be worshipped by the protohumans, and declares he is "happy at last".