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The Turtles are out looking for Splinter while they are attacked by the Foot on the roof of a building. They fight and win but Mikey is badly cut on his arm. The Turtles see a building with the logo "TCRI." They remember that the canister of ooze that mutated them had the same logo. The Turtles decide to return home and patch up their wounds. Donatello looks for information about TCRI but cannot find anything even saying that it exists.
The Turtles return to the building but find that there are no entrances or exits except for the one on the roof. They break into the building using Donatello's expertise to open magnetic locks and a puppet to trick the security system. The first four levels are hallways with only a small window and an entrance and an exit door. On the 5th floor from the roof they find a room and obtain a keycard. They hide from two passing individuals talking about leaving Earth. Then they continue down the level and try a random door. They stumble upon a Splinter that is unconcious and hooked up to a machine.
They are discovered inside the room and several machines run by brain-like aliens fire upon them trying to stun them. The Turtles retreat to a room that the aliens do not want them to go into. Mikey tried to climb up some wires in the room but he fell onto the controls for the equipment. This activated the equipment and it cannot be shut down.
A reprint in 1987 had an 8 page story included.