When the ship known as the USS ENDEAVOR mysteriously loses contact with the mainland, the CIA puts Byron Danvers and Patricia Hartley in charge of leading an expedition to rediscover the missing vessel. The vessel was investigating the mysterious melting of a two mile deep frozen lake, possibly by global warming. Their first matter of duty is finding a captain to lead them into the Arctic seas. They find Captain Steven Jenkins at “The Last Stand Bar”, where he drunkenly agrees to go on the mission.
While there, the group rendezvous' with the U.S. nuclear submarine the COPLEY. The two groups compare missions with the Captain of the Copley and decide to go the abandoned drill base camp.
Onboard the “Icebreaker” ship known as The AUSTRALIS, Danvers and Jenkins joke about the possibility of an underwater kingdom, similar to Atlantis, that once existed millions of years ago. Upon discovering The ENDEAVOR, Jenkins, Danvers, and two Navy Seals go on a search mission to retrieve any data and save any survivors after rendezvousing with the U.S.S. nuclear submarine the COPLEY. They compare missions with the Captain of the COPLEY and decide to go the abandoned drill base camp.
But first, they enter the abandoned ENDEAVOR. The two navy seals enter the engine room and see nothing but blood on the ground. Eventually, they discover Captain Phillips, who warns them of a creature lurking behind him. They are killed by the creature, only Jenkins, Danvers, and Hartley make it back to the AUSTRALIS.
Onboard, Danvers admits that he hopes to find some tablet to reveal that life once existed beneath the surface. They receive orders to dig into the arctic ice and discover what lurks beneath. They drill into the ice and go on another search and discovery mission. They are attacked and captured by creatures that resemble the human form,
but are seven feet tall and covered in slime.
Danvers attempts to communicate with the creatures. They watch in horror as the ship’s first mate, Willie, is literally absorbed into one of the creature's bodies.
Danvers is revealed to be a traitor who has been working with the creatures the entire time. Danvers also reveals plans to detonate a nuclear bomb from the COPLEY to melt the polar ice caps and melt the frozen lake, releasing millions of creatures to kill whoever’s left.
Hartley and Jenkins manage to escape. After fighting off many creatures with a mere harpoon, and make it to the engine room where Danvers is about to set off the bomb, at the “Master Being’s” command. Hartley and Jenkins manage to get the “Master Being” positioned in front of a torpedo that they fire in his direction, dragging it and the Being along into the ocean. The torpedo detonates a few miles away.
After the explosion blows up underwater and miles away it raises the ocean and the vessels out of the water to come crashing down back into the water. The explosion melts some ice , but because it blew up so far away, the lake trapping the Beings did not melt, keeping them trapped forever.
Back on-board the AUSTRALIS, heading home, Hartley and Jenkins get together and kiss.