Though Megatron had been vanquished, Shockwave has led the Decepticons to near-total control of Cybertron. Cobra Commander, meanwhile, plots to take control of the Cybertronian supercomputer Teletraan 3. His scheming and interference, however, causes the computer to go berserk, transporting random groups of Transformers through time and space. Teams of allied Joes and Cobras must follow the displaced robots and return them to the present, before their presence will cause a time storm to scourge Earth.