The "Plague ship" was an Autobot starship whose entire crew was infected with Cybonic Plague. After the crew died, the ship apparently crashed onto Earth where it became buried in the sand dunes of a desert.
Centuries after it crashed, the ship was uncovered and the distress signal that it was broadcasting was able to be received by the Autobots on Earth. Ratchet and Optimus Prime investigated the wreck. Once inside, Ratchet found out that the crew did not die from attack, but from a virus. Both he and Optimus began to leave the ship but a tremor knocked down a corpse that leaked infected energon onto Optimus, infecting him with Cybonic Plague.