Nemesis is the fifty-first and fifty-second (also the final two) episode of the Beast Wars TV series.
The Maximals, secure for the first time since they moved into Mount St. Hilary, begin searching for the Predacons, who have been vulnerable since Tigerhawk destroyed the Predacon base. Optimus Primal quotes a verse from the Covenant of Primus, believing Tigerhawk's arrival to be divine prophecy.
Meanwhile, the Predacons are growing disaffected with Megatron. (Even Waspinator is mouthing off.) Inferno, ever loyal to his "queen", declares that a new "colony" will resecure them. Megatron orders him to take Waspinator and Quickstrike, while he, Rampage, and Dinobot search the remains of Tarantulas's lair. Dinobot finds a hatch which leads to an underwater tunnel and a computer. Accessing the computer, Megatron becomes quite excited by what he discovers, and takes the rail car with Dinobot II, while Rampage follows in tank mode.
Silverbolt and Depth Charge spot Inferno, Waspinator, and Quickstrike leaving. Optimus orders them to fall back, but Depth Charge heads in. Optimus leaves with Blackarachnia, Cheetor, and Tigerhawk to support them. As Primal arrives, Depth Charge finds the hatch—and a bomb. The explosion fails to kill any of the Maximals, but Silverbolt is damaged, and Blackarachnia and Cheetor escort his parts back to base.
At the protohumans' cave dwellings, Inferno declares that the caves will be their new "colony". He orders Quickstrike and Waspinator to engage, but Waspinator angrily refuses. Something has finally snapped in Waspy's central processor, and he declares that he is out of the Beast Wars. After a tirade against Megatron, the Predacons, life in general, and always being blown up, Waspinator tells them that they can kiss his stinger. Inferno and Quickstrike blast him, and proceed to attack the protohumans (who have become much tougher, having learned from the example of Dinobot and the Maximals).
In the tunnels, Primal, Tigerhawk, and Depth Charge continue searching. After locating a data terminal, Primal accesses it and discovers what Tarantulas found and Megatron desires—the Nemesis, the flagship of the Decepticon fleet and the vessel which Megatron used to shoot down the Ark. Realizing the threat the Decepticon warship holds, Depth Charge heads out to locate it. Optimus sends out an emergency warning to the Maximals, and he and Tigerhawk head out to the Nemesis's location through the air.
Meanwhile, Megatron and Dinobot are able to board the ship, where they discover that Tarantulas had been a busy spider: not only did he repair the vessel, he added a transwarp cell and installed a Predacon control console. Best of all, in Megatron's optics, Tarantulas left behind a copy of the Covenant of Primus to boot: the tome from which he took his name! Megatron and Dinobot begin powering up the vessel for an attack.
Reaching the sunken behemoth, Depth Charge informs Optimus of his discovery, and Optimus in turn authorizes Depth Charge to neutralize the Nemesis by any means necessary. Before Depth Charge can start, he is engaged by Rampage. The two enemies fight, and Depth Charge grabs an energon crystal. He drives it into Rampage's spark, and the explosion destroys both Transformers and also causes Dinobot to cry out in pain. Optimus, though mourning Depth Charge's loss, is relieved to know the threat of the Nemesis has been dealt with.
That is, until the Nemesis rises from the ocean, fully operational.
Megatron has raised the Nemesis from its watery grave and has begun a random attack on everything in sight, all the while quoting the Covenant of Primus. After telling Rhinox to "deploy Operation Eternity", Optimus Primal and Tigerhawk attempt to fight it off, but their weapons don't even scratch the hull. Tigerhawk tells Primal to rally the Maximals and that he will remain to fight. On the Nemesis, Dinobot is commenting that his spark has changed and feels complete. Aspects of the original Dinobot begin to emerge. He admires Tigerhawk's defense. Tigerhawk is able to damage power on several decks, limiting Megatron's offensive options to using the fusion cannon, which he uses to destroy Tigerhawk. Going to the Protohuman settlement, Megatron prepares to destroy it. Dinobot objects, asking where the honor is in such an act, but Megatron fires anyway, killing Inferno and Quickstrike in the process.
At Mount St. Hilary, the Maximals are preparing a last-ditch strategy—bring the Ark online and fight the Nemesis. However, the ship has been offline too long, and Rhinox and Blackarachnia are having trouble restoring power. The Nemesis arrives, but Tigerhawk's attack has depleted its energon reserves, and the fusion cannon requires time to recharge. Megatron activates its tractor beam, and Primal enters the Nemesis. He and Megatron duke it out, but the Predacon clearly has the advantage. On the Ark, the Maximals manage to get the engines on line, but they burn out almost instantly. Rattrap proclaims that they are all going to die, and for once, no one tells him to shut up. Instead, the characteristically stoic Rhinox simply responds with "Yup".
However, Dinobot, disapproving of Megatron's actions, sends a message to the Maximals of an Autobot shuttle stored in the Ark. Megatron orders Dinobot to fire, but he refuses, stating that he has his honor. In a last bid to save them all, Rhinox pilots the shuttle on a collision course with the Nemesis's bridge, crashing through the viewport and going out the other side, dragging Megatron along. Optimus urges Dinobot to save himself, but he simply bids farewell to Primal and remains as the bridge explodes around him. As the Nemesis crashes, Primal rejoins the other Maximals.
Some time later, the Maximals, having restored the original Megatron's spark, repaired the shuttle and rigged a transwarp cell to it, leave Earth for Cybertron. Optimus, piloting the ship, declares that the Beast Wars are over, and memorializes the Maximals who fell during the war. Rattrap, however, is more happy to be going home and points out that they won't have to see Megatron 'til they get there, as the Predacon is tied to the hull of their shuttle. As the shuttle enters transwarp, the scene shifts to the Protohumans, who have built a village and are using parts of Inferno and Quickstrike in a ritual to celebrate their new leader...Waspinator.
Waspinator declares that he is "happy at last".