| 1. Atlantis Destroyed | not rated | 1:50 |
| 2. The Smithsonian | not rated | 1:52 |
| 3. Late for Presentation | not rated | 1:51 |
| 4. Milo Meets Heloga | 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 | 2:44 |
| 8. The Submarine | not rated | 3:20 |
| 9. Exterior Lights | not rated | 0:35 |
| 10. Leviathan battle | not rated | 3:35 |
| 11. Breaking Through the Surface | not rated | 1:10 |
| 12. The Journey | not rated | 3:24 |
| 13. Bedding Down | not rated | 2:31 |
| 14. Fireflies | not rated | 2:14 |
| 15. Atlantis Discovered | not rated | 1:45 |
| 16. Milo and Kida Speak | not rated | 3:30 |
| 17. Milo and Kida's Questions | not rated | 3:04 |
| 18. Tour of Atlantis | not rated | 2:53 |
| 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 | 3:49 |
| 23. The Crewis Conscience | not rated | 2:12 |
| 24. The King Dies | not rated | 3:35 |
| 25. Going After Rourke | not rated | 1:48 |
| 26. Dogfight | not rated | 5:01 |
| 27. Just Do It | not rated | 3:29 |
| 28. Kida Returns | not rated | 1:39 |
| 29. Goodbyes | not rated | 1:40 |
| 30. Atlantis | not rated | 2:01 |
| 31. End Credits | not rated | 2:25 |
| 1:12:53 |
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