The film starts in Underwater Ruins, with General Temato invading an old temple and killing some monks. He finds a mural with a map to Atlantis and the picture of a Leviathan.
Tadeo Jones visits his mother on an asylum to invite her to his wedding with Tadea Croft. After some wacky hijinx, the Mummy crashes the wedding and makes the couple wanting to go on a honeymoon vacation without the comic reliefs. They travel to Barcelona, but as soon as they arrive to the hotel, the funny side characters escape from the suitcase and follow them.
Everybody goes to the Sagrada Familia and discover a map similar to the one in the beginning after the Mummy fights with a random Catalonian called Dasuiso. Everybody but Tadea want to follow the map to Atlantis because Tadeo thinks his missing father will be there. So she returns home while the rest pick a boat.
The boat sinks and they are saved by a mermaid who gives them Super Not-Drowning Skills and shows them Atlantis. General Temato plans to take the Prongs of Poseidon to Take Over the World with tsunamis. He kills the leader of the merpeople and takes the Trident. Tadeo steals it and runs away, but Temato recognizes him as his son.
All the secondary characters become hostages in Atlantis and Temato kidnaps Tadea and the girl from the second film. This convinces Tadeo to change the Trident with his friends and Temato uses its Mind Control abilities to invoke a Leviathan. To save their families in Spain, his henchmen join Tadeo and turn their giant submarine into a Humongous Mecha.
Tadeo and Tadea reconcile to control the submarine robot and stop the Leviathan. But a tsunami is already going to Spain and Tadeo can only stop it taking the Trident from Temato. He exits the robot and does it, stopping the tsunami. Temato is imprisoned and Tadea is pregnant.
