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The Shell Sub is a submarine used by the Turtles in the 2003-2009 animated series. Donatello had spent several weeks creating an outlet from the Turtles' lair to the river, and constructed a small submarine - large enough for two people to comfortably ride - that he christened the Shell Sub. Despite being a primarily exploratory vehicle, the Shell Sub is equipped with various projectile weapons.
Its maiden voyage in the episode Junklantis was problematic. Donatello ventured out into the harbor with Michelangelo, and the small sub was soon captured by the Garbageman's whale-shaped submarine. They eventually escaped in the Shell Sub just before the whale submarine crashed into Junklantis, but were pursued by the Garbageman and the Shell Sub was badly damaged. They eventually made it back to the lair.
Donatello was in the process of making repairs to the Shell Sub when Karai and the Foot attacked the lair. Donatello and Splinter escaped the lair in the Shell Sub, but they were pursued in the river by Foot Ninja on underwater vehicles. Though Donatello and Splinter managed to escape, the Shell Sub was destroyed. Scion of the Shredder