After defeating the Foot Clan and Hun in an attack on Oroku Saki's skyscraper, the Turtles find that Master Splinter has vanished. A lead takes them to a building marked T.C.R.I., where they discover the employees are Utroms — a brain-like alien race — and are accidentally teleported across the galaxy. They arrive on D'Hoonib, meet the Fugitoid Professor Honeycutt, and are pulled into the war between the Triceratons and the Federation, both after Honeycutt's technology. They also encounter Slashuur, a legendary intergalactic bounty hunter contracted to capture Honeycutt. After defeating him, the Turtles free a noble Triceraton warrior named Traximus from forced gladiatorial combat and eventually make it back to Earth.
There, the Utroms reveal they rescued Splinter and have been caring for him. Using a VR machine, they explain their history: they crashed in feudal Japan while transporting the dangerous rogue Utrom Ch'rell, who escaped and became the origin of the Shredder identity. Baxter Stockman sabotages the VR machine mid-session, making the simulated dangers real. Once the Turtles escape the simulation, they find the current Shredder — revealed to be Ch'rell himself — attacking the T.C.R.I. building. Ch'rell is defeated before he can follow the Utroms through their Transmat, and a destruction device levels the building. The Turtles get out in time.