Rob and the Orbots are onboard the Stellar Queen to see off Rondu and Dia. The Orbots sneak a peek at the ship's anti-matter engine, and Bort's clumsiness almost wrecks the machine. While the disaster is averted, Bort's already fragile confidence is shattered.
Unfortunately, space pirates, led by Captain Shrike, capture the luxury liner. They move all of the passengers to their own ship, as well as the anti-matter engine. They also hook Rondu up to their master computer, wanting to use his unique life force as an energy source.
Dia manages to get a message to Earth, and Mighty Orbots quickly chases them down. Shrike uses the anti-matter engine as a weapon against Mighty Orbots, who is flung at the sun. Crunch detaches and eats enough debris to give Mighty Orbots a power boost, and they manage to escape their fate. Shrike then uses Rondu's energy to create a creature called a Thetan, which he then sends against Mighty Orbots. Mighty Orbots manages to split the Thetan into five smaller Thetans, and then the individual Orbots fight and defeat the Thetans.
Not willing to accept defeat, Captain Shrike uses his master computer to create a super Thetan, considerably larger than the Thetan from before, and sends it after the Orbots. The Orbots are trapped within the debris and the Thetan hurls an energy beam at them. Bort takes the form of a deflector dish and shoots the energy back at the Thetan and back into the anti-matter engine. The Thetan is destroyed, and Rondu is restored. Unfortunately, all this has caused a chain reaction which will destroy the anti-matter engine and everyone else as well. Everyone gets back on the Stellar Queen and Mighty Orbots manages to push the ship to safety.