The third and final specially edited memorial episode featuring Jean’s narration. This is a breath-taking sea adventure action animation. The story centers on a series of critical battles by the indestructible submarine, Nautilus and the conflict between Captain Nemo and the Gargoyle. It’s a shorter, more streamlined version of Nadia called "The Nautilus Story", which all but eliminates the filler arc and concentrates on the struggle between Nemo and Gargoyle. Some scenes in the more pivotal episodes are cut as well. The compilation series was made by Hideaki Anno, who was said to have been dissatisfied with the final result of the TV show. The Nautilus Story was only released in Japan on VHS and laserdisc.
| Directing | Hideaki Anno | Director |
| Sound | Shiro Sagisu | Music |
| Visual Effects | Toshiyuki Kubooka | Animation Director |
| Visual Effects | Yoshiyuki Sadamoto | Character Designer |
| Writing | Jules Verne | Original Concept |
| Directing | Shinji Higuchi | Director |
| Art | Masahiro Maeda | Settings |
| Art | Masanori Kikuchi | Art Direction |
| Art | Hiroshi Sasaki | Art Direction |
| Writing | Jules Verne | Novel |
| Writing | Hideaki Anno | Story |
| Writing | Hayao Miyazaki | Story |
