Dr. Wily and his robots launch an attack on an underwater mining operation, but Mega Man was able to save it, just barely. As a showing of gratitude, Eugene Peister, the administrator of the mine, rewards Dr. Light with a brand new lab. While Dr. Light and Roll are in awe of the new place, Mega Man has a feeling that this is all too good to be true, and it is. The "new lab" is really a walking vehicle meant to deliver the heroes to their doom, deep underwater. But a savior comes in the form of... a squid?!
- This was the season finale.
- Eugene Peister is voiced by Jay Brazeau.
- The lab complex-turned prison is reminiscent of the AT-AT walkers in The Empire Strikes Back. But, there is no reason to believe that this was an actual reference to the movie.
- The name of this episode is an obvious take on the novel 20,000 Leagues Under the Sea.
- During the first battle, the Rolling Cutter on Cut Man's head gets crushed by a large rock, a reference to his main weakness, the Super Arm.
- This was the final episode to feature a new Robot Master from Mega Man 4, as Skull Man never appeared in the show.
- Bubble Man is notably absent despite the deep sea theme of this episode.