A group of scientists find the body of Optimus Prime, and some spores that bring out aggressive tendencies with whomever makes contact with it. The scientists have a grudge against the Autobots, and use Optimus's body to lure them into a trap. As the spores spread through the Autobots and Decepticons, Rodimus orders Sky Lynx to find a Quintesson in a desperate attempt to bring Optimus Prime back to life.
The spores have spread across the Galaxy. Optimus hopes to find a cure in the Matrix, which is inside Rodimus Prime, but Rodimus has been infected by the spores. Optimus must find a way to get the matrix, without becoming infected.
Some autobots are captured. The remaining Autobots team up with some rebels to free their friends, the rebels know all the weaknesses of their enemies machines. They merge with the Autobots to become Headmasters to free their friends.
The HIVE forms an alliance with the Decepticons. Cyclonus allows the HIVE to modify the heads of the Animal Decepticons, so they can become Headmasters. The remaining Decepticons offer their weapons to become Targetmasters. After they face the Autobots, the rescued Autobots become Targetmasters.