The villain in Atlantis: The Lost Empire is Commander Lyle Tiberius Rourke. He leads the expedition’s mercenaries and ultimately betrays the explorers and the people of Atlantis.
Rourke initially appears to be the expedition’s disciplined military commander, helping guide the submarine Ulysses toward the lost city in 1914. After the team reaches Atlantis, however, he reveals that his real goal is to seize the powerful Heart of Atlantis and sell it for profit.
His betrayal places Princess Kida and the entire city in danger. Rourke captures Kida after the crystal merges with her, then attempts to transport her back to the surface. Milo Thatch and several former members of the expedition oppose him, while other mercenaries abandon Rourke when they realize his plan would destroy Atlantis.
Helga Sinclair is Rourke’s second-in-command and an important antagonist, but she is not the film’s principal villain. “Commander” is his rank, while Mole is the nickname of Gaetan Molière, the expedition’s eccentric geologist. Rourke’s full name is therefore the most precise answer.