While Michaelangelo is testing out a sailboard in the sewers, he accidentally gets swept out into the city harbor. At the same time, a captain named Talbot Breech is testing his miniaturizing ray on a ship. His plan is to shrink all the naval ships and put them in bottles for his collection in order to get even with those who turned him down for the Naval Academy.
The ray gun accidentally shrinks Michaelangelo and he winds up in a bottle along with the other ships in the captain's lab. Breech's cat, Claude, knocks Michaelangelo off the shelf, breaking the bottle and freeing him. He does not realize how small he really is until he comes nose to nose with Claude. Michaelangelo manages to outwit Calude and run away from a huge rat.
Meanwhile, in the harbor, April and Vernon are covering a story on one of the Navy's aircraft carrier. While April is in the middle of her story, the carrier begins to shrink and disappears right on TV. Donatello, Raphael and Leonardo happen to be watching April's broadcast and see her disappear. Not knowing where Michaelangelo is, they set out to help April without him.
In the Captain's lab, Michaelangelo finds April and Vernon, who are now shrunk in size like him. April helps Michaelangelo escape in one of the tiny aircrafts. He manages to find the other Turtles on the dock and thye follow him to the Captain's lab.
At the lab, the Turtles get attacked by Breech's robots, but they are no match for the Turtles. April, Vernon and Michaelangelo get zapped by the ray, turning them back to normal size. The ray also hits all of Breech's boat collection, turning them back to normal size and ruining his lab.moreless
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