It's 1914 and Milo James Thatch (voice of MICHAEL J. FOX) is a meek cartographer and linguist who wants his museum boss, Fenton Q. Harcourt (voice of DAVID OGDEN STIERS), to fund an exploration where he hopes to find The Shepherds Journal, an ancient guidebook that will provide clues to finding the long lost island of Atlantis.
Unfortunately, Harcourt and most everyone else thinks that Thatch is as crazy as his grandfather who had similar notions, and thus his request is denied. Thinks look up, however, when the sultry Helga Sinclair (voice of CLAUDIA CHRISTIAN) takes Milo to meet Preston B. Whitmore (voice of JOHN MAHONEY), a wealthy older man who knew Milo's grandfather. Having recently discovered the Journal and wishing to live up to a bet he made to that man long ago, Whitmore has decided to fund Milo's quest.
Setting out on a huge submersible run by Commander Lyle T. Rourke (voice of JAMES GARNER), Milo meets the rest of the crew including Lt. Sinclair; demolitions expert Vinny Santorini (voice of DON NOVELLO), teenage mechanic/engineer Audrey Ramirez (voice of JACQUELINE OBRADORS); ship physician Dr. Joshua Sweet (voice of PHIL MORRIS); short order cook "Cookie" (voice of JIM VARNEY); chain smoking switchboard operator Wilhelmina Packard (voice of FLORENCE STANLEY); and an odd little fellow, "Mole" (voice of COREY BURTON) who likes to burrow or spend his time in the ground.
In search of a legendary Atlantean power source that reportedly allowed for electricity and powered flight several thousand years ago, the crew battles a gargantuan leviathan and loses most of its men before arriving in the fabled land at the bottom of the sea. There they find a thriving civilization living in a protected environment and meet Princess Kida (voice of CREE SUMMER), heir to the Kingdom of Atlantis.
While she's happy about the arrival of outsiders as she hopes that they can shed light on mysteries from their past, her father, the King of Atlantis (voice of LEONARD NIMOY), isn't as he realizes that most of them are probably up to no good. As he gets to know Kida and explores the land while the King's worries prove to be true, Milo does what he can to help and protect the Atlanteans from disappearing again and forever into obscurity.