After a long journey, Mighty Orbots lands on the planet Urbanos carrying a pod containing a substance called Protean, which will grow uncontrollably if exposed to oxygen. Unfortunately, the pod is soon stolen by a pair of thieves: Kleptos, and The Kid. The Orbots try to chase them down, but come up short.
Meanwhile, Umbra contacts the Shadow agent, Belladonna, and tells her to capture the pod. She calls upon her Mutron, which has transformation abilities similar to Bort's, and they also attempt to hunt down the thieves.
While Kleptos attempts to sell the pod, The Kid finds himself in a precarious position and Crunch, not realizing who he is, saves his life. This starts a friendship between the two of them.
Rob and the Orbots finally manage to track down the thieves and are about to retrieve the pod when Belladonna appears on the scene. The thieves take advantage of the distraction to escape. Rob sends Bort and Crunch after them, and has the rest of the Orbots take on Belladonna, who is riding in a huge Shadow Walker. They come up short and are nearly destroyed in a junkyard before a last minute escape. Belladonna tracks down the other two Orbots as well as the thieves underground, but once again the thieves manage to escape. However, The Kid, paying Crunch back from before, helps him and Bort escape as well.
Kleptos decides that since Belladonna is so interested in the pod that he might as well sell it to her. Unfortunately, she double crosses him and captures him, The Kid, and the pod. The Kid winds up opening the pod and the Protean, exposed to oxygen, grows out of control. The Orbots join into Mighty Orbots and attempt to stop the rapidly growing Protean, but cannot. Rob decides that if oxygen makes the creature grow, then carbon dioxide might stop it. They are correct, and hitting it with carbon dioxide makes it stop growing and also turns it solid and harmless. Belladonna is captured, and Rob and the Orbots decide to give Kleptos and The Kid a second chance, although Rob has his doubts.