A flashback shows Jonas Taylor (Jason Statham) attempting to rescue other divers, among them Dr. Heller (Robert Taylor). Taylor rescues some but refuses to go back to save others, after he understands that going back for the rest would mean the death of all. Heller however is furious for Taylor abandoning the rest of the crew.
Around five years later, Jack Morris (Rainn Wilson) meets Dr. Minway Zhang (Winston Chao) and his daughter Suyin (Lin Bingbing) at a modern underwater research facility called "Mana One". A mission to dive further into the oceans is being conducted with Celeste (Jessica McNamee), Toshi (Masi Oka) and The Wall (Ólafur Darri Ólafsson) underwater and supervised by DJ (Page Kennedy) and Jaxx Heard (Ruby Rose) and James 'Mac' Mackreides (Cliff Curtis) at the station. The mission appears to be going well, until a large object hits the ship and causes it to lose contact with Morris, Zhang and Suyin.
Mac suggests sending Taylor down to attempt a rescue, after he suspects the object which hit the underwater ship to be Megalodon, a giant shark thought to have been extinct, to be the same Taylor encountered five years ago. Dr Heller objects, but Chang and Mac decide to travel to Thailand to recruit him anyways.
In the meantime, Suyin decides to attempt a rescue herself. Taylor follows her and ends up rescuing The Wall and Celeste . Toshi however, realizing that Megalodon would kill all crew members immediately, closes the passage to his ship and leaves to die while giving passage to Taylor, Celeste and The Wall.
Back at Mana One, the station receives a signal that sharks have broken through the depths of the ocean - including Megalodon. What follows is an attempt to track and inject poison into Megalodon. While the crew does succeed in doing that with a shark, they kill the wrong one and Megalodon attacks the crew, eating Dr. Heller and The Wall and causing a fatal injury to Zheng.
The rest moves back to the Mana One. Morris decides to take out Megalodon himself with grenades thrown from a helicopter. However, he accidentally kills a whale instead and then gets eaten by Megalodon.
Taylor and the crew realize that Megalodon is en route to a local Chinese beach, full of attendees. There, Megalodon causes havoc and eats a number of beachgoers. The crew decides to save the local beachgoers by attracting Megalodon. Taylor manages to scratch Megalodon and attract other sharks to eat it, that way killing it. Having killed Megalodon, Taylor and his crew reunite at a private boat used by a Chinese couple.