| 1. Atlantis Destroyed | not rated | 1:50 |
| 2. The Smithsonian | not rated | 1:53 |
| 3. Late for Presentation | not rated | 1:51 |
| 4. Milo Meets Helga | not rated | 0:30 |
| 5. Arriving at Whitmore | not rated | 0:40 |
| 6. The Book | not rated | 1:08 |
| 7. Whitmore Hires Milo | not rated | 2:43 |
| 8. The Submarine | not rated | 3:20 |
| 9. Exterior Lights | not rated | 0:37 |
| 10. Leviathan Battle | not rated | 3:33 |
| 11. Breaking the Surface | not rated | 1:10 |
| 12. The Journey | not rated | 3:24 |
| 13. Bedding Down | not rated | 2:31 |
| 14. Fireflies | not rated | 2:12 |
| 15. Atlantis Discovered | not rated | 1:45 |
| 16. Milo and Kida Speak | not rated | 3:31 |
| 17. Milo and Kida's Questions | not rated | 3:04 |
| 18. Tour of Atlantis | not rated | 2:54 |
| 19. Secret Swim | not rated | 2:45 |
| 20. Adventure Capitalists | not rated | 2:13 |
| 21. Storming the Palace | not rated | 1:40 |
| 22. Kida Transforms | not rated | 3:45 |
| 23. The Crew's Conscience | not rated | 2:12 |
| 24. The King Dies | not rated | 3:35 |
| 25. Going After Rourke | not rated | 1:49 |
| 26. Dogfight | not rated | 5:00 |
| 27. Just Do It | not rated | 3:29 |
| 28. Kida Returns | not rated | 1:40 |
| 29. Goodbytes | not rated | 1:40 |
| 30. Atlantis | not rated | 2:01 |
| 31. End Credits | not rated | 2:22 |
| 1:12:47 |
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