The film begins with a large tidal wave, triggered by a distant explosion, which threatens to drown the island of Atlantis. In the midst of an evacuation from the capital city, the Queen of Atlantis is caught by a strange, hypnotic blue light and lifted up into the "Heart of Atlantis", a powerful crystal protecting the city. The crystal consumes her and creates a dome barrier that protects the city's innermost district. She leaves behind a young daughter, Princess Kida (Cree Summer), as the island sinks beneath the ocean.
Ten thousand years later, in 1914, Milo Thatch (Michael J. Fox)—a cartographer and linguist (who are our heroes are working with) at the Smithsonian Institution who is marginalized for his research on Atlantis—believes that he has found The Shepherd's Journal, an ancient manuscript allegedly containing directions to the lost island. After his proposal to search for the Journal is rejected by the museum board, a mysterious woman, Helga Sinclair (Claudia Christian), introduces Milo to Preston B. Whitmore (John Mahoney), an eccentric millionaire. Whitmore has already funded a successful effort to retrieve the Journal as repayment of a debt to Milo's grandfather, and recruits Milo and our heroes to lead an expedition to Atlantis as soon as they decipher it. Victor then leaves to get something before they go.
The expedition departs with a team of specialists led by Commander Rourke (James Garner), who also led the Journal recovery expedition. The crew includes Vinny (Don Novello), a demolitions expert; Mole (Corey Burton), a geologist; Dr. Sweet (Phil Morris), a medical officer; Audrey (Jacqueline Obradors), a mechanic; Mrs. Packard (Florence Stanley), a radio operator; and Cookie (Jim Varney), a mess cook. Our heroes find Victor has come back and has brought Zecora with him, to help him with medical problems. Then Steamy, Puffy, and Shai-Shay come up and introduce our heroes to Evan, T.C., Hugs, Buzz, J.J., Socky, Skunky, Sharky, Willy, Mako, and 1206. Then to their surprise Rattlesnake Jake is with them and he asures our heroes that he's on their side now. Then Optimus Prime walks up with the Autobots. Steamy then explains our heroes will meet a few more engines later on. Then to their surprise, Trixie is there too. She states that she won't do any thing to Twilight, but Thomas threatens Trixie, if she tries to hurt his girlfriend, he'll murder her. They set out in the Ulysses, a massive submarine, onboard our heroes meet the Miner Trains, Steam Grindor, Steam Mech, Mucker: a demolitions expert and geologist, Steam Claw Digger, Steam Driller, Steam Sweeper, and Steam Excavator. Then they are soon attacked by the monstrous Leviathan, a robotic lobster-like creature that guards Atlantis' entrance. The Ulysses is destroyed, but Milo, our Heroes, Rourke, Trixie, and part of the crew escape and make their way to an underground cavern, described in the Journal as the entrance to Atlantis.
After traveling through a network of caves and a dormant volcano with Sharky leading, the team reaches Atlantis. They are greeted by Kida—who, despite her age, resembles a young woman—and discover that the Atlantean language is the basis of many existing languages (which allows the Atlanteans to understand English). Kida enlists our heroes' and Milo's aid in deciphering the Atlantean written language, long forgotten by the natives. By swimming deep within the city's submerged ruins and translating underwater murals, Milo and our heroes help Kida uncover the nature of the Heart of Atlantis: it supplies the Atlanteans with power and longevity through the crystals worn around their necks. He is surprised this is not mentioned in the Journal, but upon examination realizes a page is missing.
Returning to the surface with Kida, Milo and our heroes discover Rourke and Trixie have the missing page. Rourke, Trixie, and the crew betray Milo, and our heroes intending to bring the crystal to the surface and sell it. Rourke mortally wounds the King of Atlantis (Leonard Nimoy) while trying to extract information about the crystal's location, but finds its location for himself hidden beneath the King's throne room. The crystal detects a threat and merges with Kida. Rourke, Trixie and the mercenaries lock Kida in a crate and prepare to leave the city. Knowing that when the crystal is gone the Atlanteans will die, Milo berates his friends for betraying their consciences and ultimately convinces them to leave Rourke and Trixie and remain in Atlantis (With help from our heroes). The King explains to Milo and our heroes that the crystal has developed a consciousness; it will find a royal host when Atlantis is in danger. As he dies he gives his crystal to Milo and our heroes, telling them to save Atlantis and Kida. Encouraged by Sweet, Milo and our heroes rally the crew and the Atlanteans to stop Rourke. But first, the Miner Trains hand Rainbow, Apple Bloom, Sweetie Belle, Scootaloo, some guns and Steamy hands Applejack a spare coachgun. Then Steam Mech asks Zecora to make a potion to make some of the other engines fly and make some nitrogleceryn which she kindly does. The Transformers get their weapons ready. Optimus then lets Thomas and Skarloey ride on him.
In a battle inside the volcano, Helga and the other mercenaries are defeated, including Rourke, who is killed when Milo slashes his arm with a crystal shard and then collides with his air ship's propellers. Then as the ship falls, Twilight dangles from the deck with Trixie prepared to kill her. Then Willy picks up a harpoon launcher and shoots the harpoon into Trixie's tail, as Mucker launches a mini rocket tied to the harpoon which wraps a rope around Trixie. Then everyone fires their guns, cannons, and blasters at Trixie, blowing her up thus killing her. Twilight plummets to ground but is caught by Optimus. Then our heroes, Milo, and the others fly the crystal back to the city, the volcano erupts. With lava flowing towards the city, Kida (in her crystal form) rises into the air and creates a protective shield. The lava breaks away harmlessly, showing a restored Atlantis, and the crystal returns Kida to Milo. The surviving crew members return to the surface and promise to keep the discovery of Atlantis a secret. Milo, in love with Kida, stays behind to help her rebuild the lost empire. As our heores hang for a while, and then leave.
- Trixie will work for Rourke in this film.
- Zecora, Steamy, Puffy, Evan, Shai-Shay, Sharky, Willy (the train), the Miner Trains (Steam Grindor, Steam Mech, Mucker, Steam Claw D., Steam Driller, Steam Sweeper, and Steam Exavator), T.C., Hugs, Buzz, J.J., Socky, Skunky, Mako, 1206, Rattlesnake Jake, Optimus Prime, Bumblebee, Ironhide, Ratchet, Sideswipe, Dino, Wreckers, Skids & Mudflap, and Wheelie will guest star in this film.
- When our heroes make camp, they hear Steamy playing his fiddle, then they all find out that some of Stuingtion's Engines can play musical instruments really, really well (much to Rarity's surprise).
- This film will be dedicated to Leonard Nimoy who died at age 83, on February 27, 2015.
- Atlantis goes under
- At the Museum
- At Mr. Whitmore's Manor house/The Shepard's Journal
- Boarding the submarine
- Meeting Stuingtion's Engines
- The Sub launches
- Meeting the Miner Trains
- The Leviathan attacks the sub
- The journey begins
- Making Camp/Stories shared
- Atlantis!/Meeting Kida
- Exploring Atlantis/The secrets of the city's powers
- Returning to the surface/Rourke and Trixie betray our heroes
- The King's story of the Crystal
- The battle in the volcano
- Milo kills Rourke/the death of Trixie
- Saving Atlantis
- Milo stays/Happy ending
Songs and Soundtrack
- Friend Like Me (Mako in the Genie's place)
- I Thought I Lost You - Miley Cyrus and John Travolta (End credit song)