| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Michaelangelo Toys Around | 4 | 3 | Wednesday September 12, 1990 |
| Michaelangelo's Birthday | 3 | 40 | Friday February 2, 1990 |
| Michaelangelo, the Sacred Turtle | 5 | 18 | Saturday November 16, 1991 |
| Mister Ogg Goes to Town | 3 | 38 | Thursday December 7, 1989 |
| Mobster from Dimension X | 10 | 6 | Saturday October 19, 1996 |
| Mr. Nice Guy | 6 | 15 | Saturday November 7, 1992 |
| Muckman Messes Up | 5 | 6 | Saturday September 28, 1991 |
| Mutagen Monster | 3 | 27 | Wednesday November 15, 1989 |
| My Brother, the Bad Guy | 5 | 1 | Saturday September 14, 1991 |
| Name That Toon | 4 | 10 | Friday September 21, 1990 |
| Napoleon Bonafrog: Colossus of the Swamps | 5 | 7 | Saturday October 5, 1991 |
| New York's Shiniest | 2 | 11 | Saturday December 10, 1988 |
| Night of the Dark Turtle | 7 | 14 | Saturday October 30, 1993 |
| Night of the Rogues | 7 | 19 | Saturday November 20, 1993 |
| Nightmare in the Lair | 6 | 10 | Tuesday November 17, 1992 |
| Northern Lights Out | 7 | 12 | Saturday October 23, 1993 |
| Once Upon a Time Machine (2) | 4 | 15 | Tuesday September 17, 1991 |
| Peking Turtle | 4 | 4 | Thursday September 13, 1990 |
| Phantom of the Sewers | 6 | 12 | Saturday October 24, 1992 |
| Pirate Radio | 5 | 13 | Saturday November 2, 1991 |
| Pizza By the Shred | 3 | 41 | Tuesday February 6, 1990 |
| Plan Six from Outer Space | 4 | 1 | Monday September 10, 1990 |
| Planet of the Turtleoids (1) | 0 | Saturday August 31, 1991 | |
| Planet of the Turtleoids (2) | 0 | Saturday August 31, 1991 |
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