The resources on Planet Cybertron dried up due to the long-term war. An Autobot space exploration team aboard the Ark led by Optimus Prime left the planet Cybertron. While Megatron led a crew of Decepticons aboard the Nemesis and chased the Ark. Both Ark and Nemesis crashed on Earth due to being pulled in by the planet's gravity. The Transformers enter a long period of stasis lock due to the impact.
The immortal life force of Starscream, who died in the future of 2005, crosses time and space to reach Earth. He possesses a Predacon and attempts to take over, but fails. He returns to being a ghost and vanishes into the far reaches of time and space.
Due to the Maximals' and Predacons' interference in the Vok experiment on Earth, the Vok begin to terraform the planet. Optimus Primal sacrifices his life to stop this. As a result, Earth loses its second, mechanical moon, and the Quantum Surge is generated.
The Transformers develop two offshoot factions/species on Cybertron, the Maximals from the Autobots and Predacons from the Decepticons, all members of which begin their lives as protoforms.
The Maximals create a Transformer based on Starscream's indestructible spark. They try to use him as an immortal warrior, but his mind proves too unstable to control. This "Protoform X" massacres Colony Omicron. All its residents are killed except for the heavily injured Depth Charge, the Imperial Peace Marshal of the colony. This event sets Depth Charge on a tireless hunt for Protoform X.
Protoform X attacks and destroys Starbase Rugby. Some of Depth Charge's friends are killed.
Four stellar cycles after the massacre on Colony Omicron, Protoform X is captured and turned over to the Maximal Elders by Depth Charge. The Maximal Elders decide to place Protoform X in a stasis pod and dump him on some barren world in deep space. The mission is assigned to Optimus Primal and his ship, the Axalon.
Depth Charge travels back in time, still in pursuit of X.
As Optimus Primal and his crew return to Cybertron via transwarp with the captured Megatron, Megatron escapes. He emerges on Cybertron in an earlier time period and uses a virus bomb to conquer the planet before Primal and his crew get there. Fires of the Past
Primal and his crew are affected by the virus bomb and lose their memories and ability to transform, but through the guidance of Oracle, they are reformatted into new bodies. The Reformatting
It is revealed that Primal was sent into the past to bring organic beast bodies back to Cybertron as part of the Oracle's plan. Primal takes Megatron with him as he throws himself into the core of Cybertron, a fountain of organic energy. They die. The sparks Megatron captured are all freed, and Cybertron is reformatted into a verdant world with a balance of organic and mechanical. Endgame Part 3: The Seeds of the Future