Umbra resurrects Dr. Phoenix, a deactivated cyborg who was exiled from Earth two hundred years earlier because of his controversial experiments. Umbra wants him to find and use him Mechanagen virus, which destroys all robotic life. At first Dr. Phoneix refuses, but then agrees to do it out of revenge.
Rondu alerts Rob that a ship is approaching the Danger Zone, an area in space which acts as a junkyard for outlawed experiments and machines. Rob and the Orbots head out to investigate. Meanwhile, the ship which is approaching belongs to Dr. Phoneix, and at Umbra's orders he activates a cloaking device to avoid the Orbots' detection. The Orbots search through the garbage, and Dr. Phoneix manages to find the canister containing the Mechanagen. Bort sees the canister being drawn into the invisible ship, and he and Tor chase after it. As Dr. Phoenix's ship takes off, the canister is breached and some of the Mechanagen gets on Ohno, infecting her and making her sick. After returning to Earth, Rondu diagnoses Ohno as having Mechanitis, a sickness brought on by Mechanagen, and tells Rob that he doesn't know how to cure it but they can at least put the virus into stasis. Rob sends Boo to retrieve the device. Meanwhile, Umbra has altered the Mechanagen, and Dr. Phoneix releases the virus all over the city. The mutated virus can now change any machine into a living, vicious monster. The remaining Orbots head out to fight the mutated machines.
Boo returns with the stasis device, and they manage to slow the virus's effects on Ohno. They form Mighty Orbots and leave Earth. Rondu surrounds the infected machines with a force field to keep them from spreading the virus. Mighty Orbots catches up with Dr. Phoenix's ship but unfortunately is captured and pulled inside. Umbra plans to use the Mechanagen on Mighty Orbots and turn the hero into a tool for evil. Mighty Orbots finds the inside of the ship too cramped, so the Orbots separate and are quickly surrounded by a force field. Dr. Phoenix tells them his plans, then has second thoughts when he learns that the world has changed in the past two centuries and now humans and robots live in peace. He stands up to Umbra, who as punishment subjects him to the Mechanagen, turning Dr. Phoenix into a complete machine. Dr. Phoenix now works with Rob to create a cure, which is used to save both Dr. Phoenix and Ohno. Furious, Umbra deactivates Dr. Phoenix and releases the Mechanagen within the ship, bringing the whole place to life. The Orbots once again form Mighty Orbots and lure the living space ship to the moon, tricking it into crashing into a mountainside. At the end the cure has neutralized the Mechanagen all over the city, and although Dr. Phoenix will have to pay for his crimes it will be taken into account that in the end he did help the Orbots and created a cure.