A boy, Miles Bennett, out partying and wake boarding at night with his friends sees something else with him in the water. A missing nuclear sub turns out abandoned and far from where it was last noted. An oceanographer's dive reveals unexpected results. A carcass washes ashore in Sullivan's Island, South Carolina.
Miles tries to befriend the unknown species he's taken in but it causes havoc at a party thrown by his sister. Laura and Rich try to make contact with the washed ashore carcass.
Lee and Cirko believe that the species that has started to reveal itself might be a force behind a trend of global warming. Miles continues to care for his creature.
Cirko presents his initial findings to a government panel even as the Earth's climate starts to chance. Daughtery goes looking for the species after learning that squid have been showing up dead with no whales to consume them. Rich continues to have visions and "communicate" with his missing brother.
The dog disappearance leads animal control to Miles and Phil. Rick goes to visit Laura in Sausalito and they find the creature she tagged has moved inland and videotape it alongside a crowd of people.
Cirko believes he's discerned the origin of the species, but is struck down by a van. Laura is brought to the hospital to identify Cirko after police discover her business card on him.
Lee must justify Cirko's death to those above him. As Laura and Richard try to evade government capture, Miles tries to evade local authorities.
Laura and Connelly build a submersible in order to visit the creatures undersea. Miles faces punishment for all his activities in trying to save Nim. Laura and Connelly sink down into the sea when they lose control of their dive.
Laura and Rich discover that the species has laid many eggs deep in the ocean. More species related deaths begin to surface even as Miles is caught in an attack.
Laura and Rich resurface from their dive to find themselves alone in the ocean. Nimrod returns. Miles passes out in class and is rushed to the hospital. Nimrod heals Miles from his wound, but is shot after he flees. Laura and Rich are rescued by the Coast Guard.
Laura and Rich try to secret themselves out of the hospital with footage of the creatures before Lee can find them. Miles learns that Nim is not dead.
Lee's men track Laura and Richard to their hotel room. Laura finds a person with supposed creature knowledge but Richard worries that it's a trap. Miles worries that the creatures have somehow changed him. Laura accompanies a female pilot who turns out to be the mysterious person, but has to leave Richard behind. She takes responsibility for the creation of the creatures.
Richard returns home to find his wife meeting with a divorce lawyer. Upon learning that the species was created by scientists, Laura tries to figure out who is ultimately behind it. Drugged Laura is rescued by Richard. The town ponders its fate as creature eggs start to appear in numbers.
Richard and Laura decide to seek out Lee to get more information, but it's Lee that learns of his origins. Laura leaves Richard to spend time with her son. Miles starts to act more like the creatures, leading to fear, anger and distrust. A crowd nearly gets away with Miles before news of a tsunami spreads.
The people of Wilmington have to leave their homes behind to avoid a tsunami. Miles abandons his parents on the escaping ferry to go back to rescue Caitlin even as Laura tries to save Richard. Miles, Caitlin, Richard, Laura and Nim hole up in a church as the tsunami hits.