Siobhan, a PhD student studying deep sea faunal behavioral patterns, signs onto the fishing trawler the Niamh Cinn Óir, crewed by six others: Captain Freya and her husband/skipper Gerard, ship engineer Omid, Johnny, Ciara, and Sudi. As they depart, the Irish Coast Guard alerts them that their planned destination, rich with fish, is in an exclusion zone. Unbeknownst to the others and despite Freya's orders, Gerard takes them into the zone anyway, as he needs a large haul of fish on this outing to keep the ship afloat.
In the exclusion zone, the boat runs into an unknown, shoal-like object and stops. Omid notices strange breaches in the hull that exude a blue-green slime. Gerard thinks they are barnacles. As Siobhan has diving gear on board for her research, the captain sends her with a knife to cut the boat free. Underwater, she sees the things stuck to the boat are the tentacles of an enormous bioluminescent organism below. Gerard says they may be a newly discovered form of giant squid. The crew attempt to capture it with the net, but the creature is too heavy. While releasing the net, Johnny's sleeve is caught in the machinery. Although freed, his hand is sliced by the rope, which is contaminated by slime.
Siobhan sees another ship on the horizon. She, Gerard, and Johnny row to it, seeking help. On board, they find the bodies of the crew in the cabin, most of whom appear to have committed suicide and with one man appearing to have had his eyes removed. Gerard says they must have succumbed to "sea fever" and orders Siobhan and Johnny not to tell the others. After rowing back, they discover the creature has released the boat. They lower the nets and bring up a large catch of fish, lifting the crew's spirits. Siobhan and Johnny flirt and discover they are interested in each other. Johnny develops a fever, which Siobhan suspects is caused by an infection, but he refuses to let his hand be checked.
While the group celebrates that night, Johnny declares he is going for a swim and is stopped by Ciara and Siobhan. Seeing him rub his eyes, Siobhan checks Johnny's eyes with a flashlight and sees something moving inside. As he washes his face, Johnny goes blind. His eyeballs burst, releasing tiny organisms that slither down the drain, entering the ship's water system. He dies. Omid realizes Sudi is in the shower and tries to stop him. Thinking Omid is joking, Sudi does not turn off the water until the waterborne creatures bite him. Gerard, Siobhan, and Omid check the water filtration system and find it has been contaminated by the creatures, which have eaten through all the filters. Siobhan realizes the creatures are the larvae of the enormous sea creature, whose eggs fill the slime. Gerard steers the ship toward shore.
Siobhan experiments on a slime sample and fails to kill the larvae with UV light. She then electrifies the trawler with Omid's help, using the arc welder. This apparently sterilizes the water supply. She insists they all must self-quarantine on board for at least 36 hours, the time it took Johnny's infection to develop. She argues if any of them are infected, they risk infecting others. The others disagree, arguing Sudi needs medical attention and that they should be hospitalized if infected. Sudi dies from the infection. Siobhan disables the boat by entangling the propeller.
Everyone checks each other's eyes for parasites. Freya, Siobhan, Omid, and Ciara appear to be clear, but Gerard sees parasites in his eyes. The couple privately shares a heartfelt goodbye before Gerard kills himself. Siobhan suspects Ciara is infected and climbs up the ladder to alert the others. When Ciara tries to stop her, Siobhan knocks her off the ladder. Ciara dies.
Freya leaves alone by rowingboat in spite of Omid and Siobhan's protests. Siobhan and Omid check the water tank again and discover the sole remaining larva has grown larger and eaten through the hull to return to the ocean. As the boat begins to sink, Siobhan and Omid use white spirit to set the deck on fire. Siobhan boards an inflatable raft. Omid, who cannot swim, falls into the water and is pulled down by tentacles. Siobhan rescues him, but cuts her wrist on a tentacle. Knowing she is infected, she swims down toward the bioluminescent creature. Alone on the raft, Omid watches as help approaches.
