6 years after the 2nd film, Atlantis has been discovered around the world about rumors, and a terrorist steals the technology to terrorize the world, and now Milo turns to Hercules for help.
- Milo Thatch (Michael J. Fox) - keeps a crowd of people away from the secrets of Atlantis and hides Kida's identity, in the end, Returns to Atlantis!
- Kida (Cree Summer) - goes by the name, Katie Thatch, and wears a necklace that changes her identity with reddish brown hair and pale skin, in the end, regains the thrown!
- Gaëtan "Mole" Molière (Corey Burton) - in the end, digs a hole in Atlantis, and causes Phil to fall in the hole!
- Preston B. Whitmore (John Mahoney) - in the end, retires!
- Doctor Joshua Strongbear Sweet (Phil Morris) - he was betrayed by one of his original people, Paul, in the end, is seen with Tarzan in Africa!
- Vincenzo "Vinny" Santorini (Don Novello) - in the end,
- Audrey Rocio Ramirez (Jacqueline Obradors) - in the end,
- Wilhelmina Bertha Packard (Tress McNellie) - in the end,
- Jebidiah Allerdyce "Cookie" Farnsworth (Blake Clark) - in the end,
- Hercules (Tate Donovan) - teams up with Milo Thatch, in the end,
- Pegacus (Frank Welker) - Hercules' pet horse, in the end,
- Zeus (Rip Torn) - Hercules' father, in the end, takes a nap in the clouds!
- Phil (Danny DeVito) - Hercules' tutor, in the end, chases Mole for causing him to fall into the hole!
- Hades (James Woods) - serves as the tertiary antagonist, in the end, takes Falcon down into the Underworld for being doublecrossed!
- Cronus (Anthony LaPaglia) - the father of Poseidon, Zeus and Hades, and grandfather of Hercules, in the end, allows Atlantis to be preserved!
- Poseidon (John Rhys-Davis) - the one who created Atlantis, in the end, returns to the sea!
- Dr. Troy Falcon (Hugo Weaving) - the main antagonist and the leader of the terrorist group, the Celestials, a terrorist wearing black gloves, a black jacket, a black shirt, and black sunglasses, with brown hair, his goal is to reign the earth's core and gain the power of the crystals, he steals the technology of Atlantis, in the end, gets taken by Hades to the underworld!
- Paul Leon (John DiMaggio) - the secondary antagonist and Falcon's right-hand man, he has a goatee, and he is loyal to Falcon, he shows a rivalry with Vinny, in the end, gets eaten by the Leviathan!
- President Woodrow Wilson (David Boat) - president of the United States, in the end, makes an announcement, about Milo's heroics!
this is the second crossover since Aladdin and Hercules!
Milo's actor reprise his roles from the first movie.