A rescue team led by Jonas Taylor tries to release a group of sailors trapped in a nuclear sumbar, and Jonas notices that the hull of the submarine is damaged by an unknown creature. Two rescuers remain trapped in the damaged submarine and say they will return in a few minutes to the rescue submarine. But Jonas decides to abandon them because he fears that other rescuers will die if they wait. After leaving, the damaged submarine explodes. Jonas tries to explain that an immense creature is becoming disaster, but nobody believes it and they all blame him.
Five years later, billionaire Jack Morris meets Dr. Minway Zhang at a research unit that Morris finances. Zhang and his daughter, Suyin, supervise a mission to explore what might be the deepest section of the Marian Pit. The expedition is led by Lori, now the former wife of Jonas, Toshi and The Wall. The mission seems to work well until a very large creature hits their submersible and makes them lose contact with the base.
James “Mac” Mackreides suggests Jonas be sent to the bottom for an attempt to save the people there, citing the similarities in his story. Although Heller disagrees, Zhang and Mac decide to go to Thailand to bring Jonas to the rescue mission. Suyin tries to save herself, but a colossal squid prevents her. Before he kills her, a massive shark kills the squid. Accepting to help, Jonas ventures into the deep and faces the greatest fear in trying to save the ex-wife and other crew members.