Forced to abandon their home planet of Cybertron due to the threat of a black hole, Optimus Prime prepares to lead his Autobot warriors to Earth. Just as they are leaving, the Autobots are confronted by Vector Prime, who warns them of the threat to the galaxy if the four Cyber Planet Keys are not gathered in time. However, Megatron has plans of his own for the universe. As they embark on the search, they travel to new planets which are inhabited by different Transformer races as well as the Autobots who lead these planets.

The series was supposed to be the final installment of the Unicron Trilogy formed with the previous two series, Transformers Micron Densetsu and Transformers Superlink. However, the Japanese production did not follow through on this intent by Hasbro, scripting the series as an independent story unconnected to the preceding shows. The English dub partially modified the series to establish links back to the two series, including changes to dialogue.