| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Return of the Shredder | 2 | 1 | Saturday October 1, 1988 |
| The Incredible Shrinking Turtles (1) | 2 | 2 | Saturday October 8, 1988 |
| It Came From Beneath The Sewers (2) | 2 | 3 | Saturday October 15, 1988 |
| The Mean Machines (3) | 2 | 4 | Saturday October 22, 1988 |
| Curse of The Evil Eye (4) | 2 | 5 | Saturday October 29, 1988 |
| The Case Of The Killer Pizzas | 2 | 6 | Saturday November 5, 1988 |
| Enter: The Fly | 2 | 7 | Saturday November 12, 1988 |
| Invasion of the Punk Frogs | 2 | 8 | Saturday November 19, 1988 |
| The Catwoman From Channel Six | 2 | 9 | Monday December 26, 1988 |
| Return of the Technodrome | 2 | 10 | Saturday December 3, 1988 |
| New York's Shiniest | 2 | 11 | Saturday December 10, 1988 |
| Splinter No More | 2 | 12 | Saturday December 17, 1988 |
| Teenagers From Dimension X | 2 | 13 | Saturday December 24, 1988 |