| Rocksteady, Rowdy Rhino // Rocksteady, Rowdy Rhino (2 variants) | 54 |
| Rat King, the Chaosbringer // Rat King, the Chaosbringer (2 variants) | 53 |
| Bebop, Porcine Punk // Bebop, Porcine Punk (2 variants) | 52 |
| Baxter, Exzzperimental Zzientist // Baxter, Exzzperimental Zzientist (2 variants) | 51 |
| Commander's Plate // Commander's Plate (2 variants) | 50 |
| Michelangelo, On the Scene // Michelangelo, On the Scene (2 variants) | 49 |
| Storm of Steel // Storm of Steel (2 variants) | 48 |
| Donatello, Rad Scientist // Donatello, Rad Scientist (2 variants) | 47 |
| Wooden Cane // Wooden Cane (2 variants) | 46 |
| Humongous Fungus // Humongous Fungus (2 variants) | 45 |
| Super Combo // Super Combo (2 variants) | 44 |
| Leatherhead, Iron Gator // Leatherhead, Iron Gator (2 variants) | 43 |
| Bebop, Skull & Crossbones // Bebop, Skull & Crossbones (2 variants) | 42 |
| Heroes in a Half Shell // Heroes in a Half Shell (2 variants) | 41 |
| Donatello, the Brains // Donatello, the Brains (2 variants) | 40 |
| Swamp // Swamp (2 variants) | 39 |
| Island // Island (2 variants) | 38 |
| Island // Island (2 variants) | 37 |
| Plains // Plains (2 variants) | 36 |
| Michelangelo, the Heart // Michelangelo, the Heart (2 variants) | 35 |
| Krang, the All-Powerful // Krang, the All-Powerful (2 variants) | 34 |
| Food Chain // Food Chain (2 variants) | 33 |
| North Wind Avatar // North Wind Avatar (2 variants) | 32 |
| Krang & Shredder // Krang & Shredder (2 variants) | 31 |
| Don & Leo, Problem Solvers // Don & Leo, Problem Solvers (2 variants) | 30 |
| Bebop & Rocksteady // Bebop & Rocksteady (2 variants) | 29 |
| Casey Jones, Vigilante // Casey Jones, Vigilante (2 variants) | 28 |
| Splinter's Technique // Splinter's Technique (2 variants) | 27 |
| Mondo Gecko // Mondo Gecko (2 variants) | 26 |
| Krang, Master Mind // Krang, Master Mind (2 variants) | 25 |
| Kitsune's Technique // Kitsune's Technique (2 variants) | 24 |
| The Last Ronin's Technique // The Last Ronin's Technique (2 variants) | 23 |
| Technodrome // Technodrome (2 variants) | 22 |
| Krang, Utrom Warlord // Krang, Utrom Warlord (2 variants) | 21 |
| Leonardo, Sewer Samurai // Leonardo, Sewer Samurai (2 variants) | 20 |
| Turtle Van // Turtle Van (2 variants) | 19 |
| The Ooze // The Ooze (2 variants) | 18 |
| Raph & Mikey, Troublemakers // Raph & Mikey, Troublemakers (2 variants) | 17 |
| Raph & Leo, Sibling Rivals // Raph & Leo, Sibling Rivals (2 variants) | 16 |
| Mikey & Don, Party Planners // Mikey & Don, Party Planners (2 variants) | 15 |
| Lessons from Life // Lessons from Life (2 variants) | 14 |
| Michelangelo, Game Master // Michelangelo, Game Master (2 variants) | 13 |
| Zog, Triceraton Castaway // Zog, Triceraton Castaway (2 variants) | 12 |
| Spicy Oatmeal Pizza // Spicy Oatmeal Pizza (2 variants) | 11 |
| Slash, Reptile Rampager // Slash, Reptile Rampager (2 variants) | 10 |
| Raphael, Tough Turtle // Raphael, Tough Turtle (2 variants) | 9 |
| Splinter, Hamato Yoshi // Splinter, Hamato Yoshi (2 variants) | 8 |
| Shredder's Technique // Shredder's Technique (2 variants) | 7 |
| Pain 101 // Pain 101 (2 variants) | 6 |
| Mind Transfer Protocol // Mind Transfer Protocol (2 variants) | 5 |