|Publication date||May 1999|
| Preceded by|
| Followed by|
MEG: Primal Waters
It has been four years after the events described in the first novel. Jonas Taylor, now married to Terry Tanaka, is working at the Tanaka Institute. Angel, the young Megalodon from the last book, has reached adulthood and is being held at the institute, which is now under the control of energy mogul Benedict Singer and his loyal assistant Celeste after being forced bankrupt by lawsuits resulting from Angel's mother's rampage at the end of the first novel. However, Angel manages to escape after killing three teenage boys who decided to sneak into a walk area surrounding Angel's tank. They harass her, and in return, she kills them by smashing the Plexiglas barrier, killing two immediately, and soon eating the third one. Jonas, with the help of his friend Mac, jumps into Angel's tank, where he discovers it is damaged and full of great white males hoping to impregnate her. Jonas realizes Angel is attracting the males by giving off a scent that is usually emitted during estrus, which she is going into. One of the males attacks and nearly kills Jonas. Mac hauls him out of the water, patches up the bite wound, and fires a transmitter dart into Angel's hide right before she bursts through the gates and escapes. Jonas is rushed to the hospital, afterwards realizing he nearly died. Masao Tanaka, Terry's father and former owner of the institute, is not coping Angel's escape and knowing she's tasted human blood. Angel begins to look for the Trench through instinct, wreaking havoc in her path, including killing several people and whales, including a whale released into the sea by Sea World named Tootie, who later becomes Angel's lunch. Jonas pursues along with Celeste and an egotistical scientist named Michael Maren, who is secretly working with Celeste and is in a relationship with her. Celeste attempts repeatedly to seduce Jonas into revealing the location of an area in the Pacific's Mariana Trench called the Devil's Purgatory, where he did top secret dives with the navy and first encountered fearsome Megalodon but she fails. After many attempts to recapture Angel, which all end in failure and at least one death, they manage to track her path and conclude she is heading for the Pacific Ring of Fire, and then she will enter the Trench.
Meanwhile Terry is tricked into boarding Singer's gigantic deep sea research station, the Benthos, to check sonar records of the mysterious implosion of one of Benedict's research subs, the Proteus, which was exploring the trench. While there she finds herself at the mercy of Singer and his sadistic Russian crewman Sergei. Once in the Trench, they find a prehistoric monster called Kronosaurus that has evolved to hunt in packs and has evolved gills. Terry manages to kill Sergei in the airlock after he attempts to rape and kill her. Afterwards, his body is eaten by the Kronosaurs, along with the remains of Captain Hoppe, a captain who planned to meet with Terry to discuss stealing a sub, called the Epimethius, and heading to the surface to exploit the suspicion of Singer's real mission, which was falsely believed to be the distribution of UNIS robots. She boards the Epimethius on its next expedition, but it is ripped apart by Kronosaurs. Meanwhile, Jonas is nearly killed on a mission to find Angel, where he attempts to find Angel in a Zodiac, but he is nearly murdered out of caution by the ship's mate, Harry Moon, and Angel after attempting to sedate her with seal carcasses filled with anesthetic. Jonas, who had nightmares about dying in the Trench, was rushed to the hospital, where he nearly died. He vows to stop his obsession with Megs and live a regular life. However, Celeste manages to use a drug to get the location of the Devil's Purgatory and heads to the Benthos where Terry has stumbled upon an undersea operation led by Benedict Singer to exploit rocks containing the rare gas Helium-3 to create fusion, located in the Devil's Purgatory. Jonas follows, along with Angel, who has made it to the Trench. Jonas goes into the Trench within an Abyss Glider submersible while Celeste paralyzes Singer, leaving him to die at the maw of a Kronosaur as revenge for killing her mother. However, he tells her her father couldn't impregnate women, so he impregnated Celeste's mother for him, thus revealing Celeste is Singers daughter. This does not stop her, however, and Singer last words are, "I'll see you in Hell." The walls of the room Singer is in are destroyed, killing him and the Kronosaur. However, this ends up destabilizing the Benthos in the process. Jonas lures Angel into killing Celeste as she tries to escape on board one of Singer's subs, the Prometheus, with the rest of the crew and rescues Terry, who was nearly killed by Celeste in the air lock like Sergei was. She survived by unlatching a barrel containing a UNIS robot with the corpse of Heath Williams, a paleo-biologist who assisted Terry with avoiding Sergei's assaults. She seals herself in the UNIS and nearly suffocates, but Jonas frees her, also killing a Kronosaur via pressure changing in the environment it was in and causing its head to implode. On their way up to the surface, the last Kronosaur attacks Jonas and Terry, but they are saved by Angel who kills the prehistoric marine reptile. The book ends with Angel giving birth to two pups, which flee into the Trench.
- Interestingly, Osama Bin Laden is also mentioned as one of the financial bankers of Benedict Singer, the main antagonist. Michael Maren returns in Primal Waters as the main villain, seeking revenge on Jonas for killing Celeste. Angel's two pups also return, one being used as a weapon by Michael, who has dubbed this Meg Scarface due to vicious scars gained in a territory dispute with another Megalodon.