1. Things Change
2. A Better Mousetrap
3. Attack of the Mousers
4. Meet Casey Jones
5. Nano
6. Darkness on the Edge of Town
7. Way of Invisibility
8. Fallen Angel
9. Garbageman
10. The Shredder Strikes Pt. 1
11. The Shredder Strikes Pt. 2
12. Unconvincing Turtle Titan
13. Notes from the Underground Pt. 1
14. Notes from the Underground Pt. 2
15. Notes from the Underground Pt. 3
16. The King
17. The Shredder Strikes Back Pt. 1
18. The Shredder Strikes Back Pt. 2
19. Tales of Leo
20. Monster Hunter
21. Return to New York Pt. 1
22. Return To New York Pt. 2
23. Return To New York Pt. 3
24. Lone Raph & Cub
25. Search For Splinter Pt. 1
26. Search For Splinter Pt. 2
27. Turtles In Space, Pt. 1 "The Fugitoid"
28. Turtles In Space, Pt. 2 "The Trouble With Triceratons"
29. Turtles In Space, Pt. 3 "The Big House"
30. Turtles In Space, Pt. 4 "The Arena"
31. Turtles In Space, Pt. 5 "Triceraton Wars"
32. Secret Origins Pt. One
33. Secret Origins Pt. Two
34. Secret Origins Pt. Three
35. Reflections