Two days after the events of the first film, Sarah (Shauna Macdonald) is washed away to safety with no memory of the events of the last time she was in the cave. She is taken to a hospital, where it is revealed some of the blood on her matches that of Juno Kaplan (Natalie Mendoza). Sheriff Vaines (Gavan O'Herlihy) demands that along with his deputy Elen Rios (Krysten Cummings), Sarah and three specialists - Dan (Douglas Hodge), Greg (Joshua Dallas) and Cath (Anna Skellern), must go back into the cave to find the missing women. A new entrance is found with the help of a sniffer dog. The team members are sent down via an old mine shaft operated by the old, mysterious Ed Oswald (Michael J. Reynolds).
Whilst crawling through a narrow tunnel in the caves, Sarah has a flashback of what happened in the caves, and in a nervous panic, attacks Vaines, Greg and Elen and runs off deeper into the caves. Vaines pursues Sarah but eventually runs into a crawler and fires a shot that causes part of the cave to collapse, separating Cath from the rest of the group. Elen, Dan and Greg arrive in a room full of bones where they find the video camera used by Holly in the first film. They watch the playback, which reveals the women were attacked by the cave dwelling 'crawlers.' Then, the three are attacked by a group of crawlers and separated.
The trio split, and Elen starts calling for help, alerting the crawlers to her location, but is stopped by Sarah, who warns Elen that the crawlers hunt via sound. The two then watch as a crawler attacks and kills Dan, ripping his throat open and dragging him away. Later, Cath escapes and kills a crawler and runs into Greg. The two climbing away from a crawler and using their radio to divert the pursuing crawler away from them. They travel deeper into the cave and find Sam hanging lifelessly. They decide to try to use her to swing across the chasm, but are both attacked by crawlers. Greg falls below, whilst tackling a female crawler, and although Cath makes it to the other side, she is attacked and killed once she gets there.
Elen and Sarah wander deeper into the cave, and kill another crawler before Elen reveals she has a daughter, which makes Sarah more determined to escape. Vaines is wandering around the cave and is about to be killed by a crawler before he is saved by Juno, who is revealed to be alive and an expert in hunting the crawlers. Elen and Sarah crawl through a tunnel and, escaping a crawler, fall into a communal defecation grounds pool. Later, all four meet up again. Juno and Sarah immediately fight, but then they all decide it's best they work together to escape and survive. Juno leads them off into the feeding pit, which she claims is also the exit. Vaines handcuffs Sarah to him so she can't leave them to die like she did to Juno. As they progress, Vaines falls over a ledge, and Elen cuts off his hand to save Sarah from falling as well.
At the film's climax, Elen, Sarah and Juno reach the exit, but are blocked by a small group of crawlers. As they try to tip-toe around the crawlers, Juno is grabbed by a dying Greg. Juno screams in surprise, which gets the attention of four crawlers. Greg dies and the women are left to fight off the crawlers. The battle is tough, but Elen, Sarah and Juno kill a crawler each. After that, Sarah sees that Juno is losing the battle to a crawler larger than the others and strangles the crawler from behind. Tensing up, the crawler rips into Juno's stomach, mortally wounding her. She and Sarah finish it off before Juno dies in Sarah's arms. As Sarah mourns for her loss, Elen turns around to leave, but finds them surrounded by a large group of crawlers. Sarah, with nothing to lose, screams to draw attention to herself, allowing Elen to escape.
Elen reaches the outside and is about to call for help when she is attacked by Ed, who hits her with a shovel and drags her back to the entrance to be food for the crawlers. As Elen recovers from the hit, a bloodied crawler jumps out at her as the movie ends.