Season 2[edit]
Megatron recruits Orion Pax, who has no memory of the Autobot-Decepticon war, into the Decepticons by lying about the Autobots being evil. Jack and Arcee travel to Cybertron to find the legendary super-computer Vector Sigma, and the Autobots successfully restore Optimus's memories with the information stored inside it. With the departure of Starscream and Airachnid, and the murder of Breakdown, the Decepticons suffer a prolonged period of infighting as Megatron struggles to keep his troops in line. Having been convinced by the events of the first season finale that Megatron is beyond hope of redemption, Optimus has resolved to kill Megatron at any cost, a choice he still struggles with in the season. The main theme for the majority of the second season is the discovery of ancient relics and weaponry from Cybertron buried on Earth, with the Transformers fighting over each new discovery. Among the relics hidden on Earth are the four Omega Keys, which activate the Omega Lock, an ancient machine capable of making Cybertron habitable again, as well as Elemental Symbols, which can give Transformers secondary personas. The Autobots each earn a new persona upon successful retrieval of the Symbols. The Decepticons acquire all four keys when Starscream returns to Megatron's command, and plan to terraform Earth into a mechanical planet like Cybertron, which would kill all life on Earth. Optimus Prime destroys the Omega Lock to save Earth, but before its destruction the Lock creates a massive fortress in the Nevada desert, and the Decepticons destroy the Autobot base with Optimus still inside.
Season 3: Beast Hunters[edit]
Following the destruction of their base at the hands of Megatron, Team Prime is scattered across the United States, and Optimus is mortally wounded from the base's destruction. Optimus believes himself to be dying and declares that Smokescreen will be the next Prime, but before the Matrix of Leadership can be passed, Smokescreen repairs him with the Forge of Solus Prime. A reformatted, much more powerful Optimus joins the battle to destroy the Decepticons' citadel with Ultra Magnus, who has reunited the team. Darkmount falls and the Autobots acquire a new base from Agent Fowler. The Autobots suffer a series of losses when the Decepticons successfully acquire a large number of Predacon fossils, intending to clone an army to conquer humanity. However, after a devastating experiment gone wrong costs the Decepticons a majority of their forces, Megatron manipulates the Autobots to wipe out the project, leaving Predaking as the sole surviving Predacon. The Decepticons refocus their efforts to rebuild the Omega Lock aboard the Nemesis with the reluctant aid of Ratchet and his Synthetic Energon. In a final battle, the Autobots capture the warship, kill Megatron, and scatter the surviving Decepticon forces. After using the Omega Lock to revive Cybertron, the Autobots bid farewell to their human friends as they leave to rebuild their home.