Subterranean by James Rollins focuses on a team of explorers who believe that they have been brought to Antarctica on a scientific research expedition. The team soon learns that they are not the first group to go under the ice to explore the abandoned dwellings. While searching for the first team, the group finds that there is an entire civilization under the ice. The explorers find that there are dangerous creatures, deadly plants, and even a member of their own team with intentions of killing everyone while they fight to get to the surface.

Ashley Carter, an archeologist, is asked to be the leader of the government's scientific expedition in Antarctica. She agrees but insists on bringing her son, Jason, who will be watched at the army base. The group also consists of Ben who is a cave explorer, Linda who is a biologist, Khalid who is a geologist and three army personnel.As they are ready to head into the vast tunnel system, Ashely is told that they are not the first group that has entered the caves and that the other group has been missing for three months. The group feels lied to, with the exception of the army personnel, but feel that they have no choice but to continue and look for the missing group.

They are in the caves a few days, following the trail of the previous group when one of the army personnel goes missing. They follow a blood trail and find that he has been eaten by a strange reptilian looking creature. They are soon attacked by several of the creatures and are barely able to escape with their lives. Ashely's group is taking refuge in a cavern, unable to contact the army base, which is also being attacked by the fierce creatures. Ashley, Ben and one of the army personnel decide to go further into the caves and leave Khalid and Linda with the other badly injured army personnel.

Ashely, Ben, and the major soon find themselves in the middle of an ancient civilization. The people, called the mimi'swee, explain that they are dying and believe it is because the humans have taken away a sacred statue from up top. Ben agrees to help, and when he gets back to the army base he finds that it has been nearly destroyed with the people nearly completely dead. Ben finds Ashley's son, who explains that Khalid has strapped a bomb to Jason's waist in order to control Linda. Khalid murdered the army personnel that had been left with him and Linda. After looking at the bomb mechanism, it is discovered that Khalid lied and the bomb can be taken off but would still have exploded.

The group is able to find the statue and replace it and Khalid dies will trying to blow up the entire cave system and kill all those left alive. The mimi'swee are saved after the humans discover that it is an mold unknown to the mimi'swee's ecosystem that has caused the problems. Ashley and Ben decide to stay with the mimi'swee for a time.