The soldiers are first seen boarding on their high-tech submarine along with their officers and the crew, as they are heading over to the bottom of the ocean to find the lost city of Atlantis. Thanks to the deciphering of the Atlantean language of the Shepherd's Journal (due to the efforts of linguist Milo James Thatch, the protagonist of the film), the crew were able to locate the lost city of Atlantis hidden underground near Iceland.
Rourke negotiates with the Atlantean King to to let him and his crew to stay one night to rest and resupply, so that they can leave by morning. As Milo talks with the king's daughter Princess Kida about the culture of Atlantis, little did he know that the soldiers are arming themselves.
Eventually, after deciphering an underwater mural, Milo finally catches onto Rourke's true motives as the latter, along with Helga and the soldiers, have armed themselves as they plan to steal the Heart of Atlantis to sell it for a good price. After locating the Heart of Atlantis (which was located under the king's chambers and fused with Kida), Rourke had his soldiers to lock up the crystallized Kida in a portable chamber and hold Milo and the Atlanteans at gunpoint to prevent them from retrieving it.
Leaving the city to be vulnerable to danger, Rourke and his army head back to the volcano's base, where they fired up a missile to create an opening through the volcano's bowels and activated a giant blimp to transport the crystal out. Fortunately, Milo and the crew, along with several Atlantean warriors, fire up several flying fish-mobiles, forcing the soldiers to fight back with with their guns and hovercrafts. At first, the soldiers had the upper hand (killing a few Atlantean warriors), but the heroes manage to use their fish-mobiles to emit crystallized bolts to take down the soldiers' hovercrafts and weaponry, effectively killing the soldiers all one by one.
Of course, Rourke didn't care about the loss of his men, even betraying Helga by throwing off the blimp to lighten the load, though this only backfired when a dying Helga uses her flare gun to destroy the blimp in revenge for Rourke's betrayal. This allows Milo to finally defeat Rourke by crystallizing him and shredding him to pieces with the blimp's propellers. Following the deaths of the Rourke and his soldiers, Milo and the crew retrieve the crystal and use it to save the city from a volcanic eruption caused by the battle.