Before D’Agosta can act on his plan, the creature attacks, killing Bailey. D’Agosta shoots the lock and forces the door open, ushering the group through. The creature attacks from behind, and the group works together to close the door against it. Smithback jams a flashlight through the door’s metal ring, locking it closed. D’Agosta has lost his radio, stranding the group without guidance. They flee to the next fork.

At the forward security station, Coffey cannot raise Pendergast or D’Agosta on the radio. A SWAT commander outlines a rescue plan involving roof entry and a rope descent into the Hall of the Heavens, but Coffey overrides standard procedure and orders the team to prioritize killing the creature over rescuing hostages.

Pendergast, Margo, and Frock reach a service shaft above the flooded subbasement. Pendergast has been unable to contact D’Agosta for 15 minutes. Margo proposes sprinkling fibers into the water to create an upstream scent trail, and Pendergast scatters them into the shaft. Frock warns that the creature can move at 30 miles per hour and will respond quickly.

In the rising subbasement water, D’Agosta admits to Smithback they are lost. The mayor persuades him that the group must stay together.

Meanwhile, Margo and Pendergast set their trap, placing the fiber bundle inside the secure area vault and hiding across the hall. Frock advises that the creature’s front legs and lower rear leg bones offer potential targets, although the shooter will need 150 feet of clear corridor. He identifies a suitable hallway near the computer room on the first floor.

The creature enters the secure area but immediately backs out, having detected the trap. When it approaches their hiding place, Margo realizes it is nocturnal and tells Pendergast to use his bright miner’s lamp. The intense light drives the creature away. Pendergast fires twice, and a blood trail reveals that D’Agosta’s group has already wounded the creature. Frock concludes that the beast is now bent on revenge.

Cuthbert tries to persuade the intoxicated Wright to hide in the dinosaur hall, but Wright refuses. Suddenly, the creature slams into the lab door. Cuthbert forces Rickman into the adjacent hall. The door splinters, and as Cuthbert accidentally fires one of his five bullets, the creature tears through. Wright finally stumbles into the dinosaur hall.

A SWAT team breaches the roof, descends to the fourth floor, and enters the Hall of the Heavens through a trapdoor. They find bodies and begin evacuation. Hearing a pistol shot from above, the commander leads part of his team upstairs, where they discover that the creature has killed Wright. Cuthbert fires wildly as the creature charges. The SWAT team apprehends the incoherent Cuthbert, who tells them the creature was eating Wright’s brain. The team enters the dinosaur hall and discovers the headless corpses of Wright and Rickman. The creature attacks. Over the radio, Coffey hears gunfire and screaming, then silence. Panicked, he orders immediate evacuation and refuses contact with Pendergast. Seventeen bodies are removed from the Hall of the Heavens. The evacuated Cuthbert tells Coffey the creature is intelligent and cannot be killed.

In the subbasement, the mayor persuades D’Agosta to organize the group in a human chain as they wade through waist-high water toward the right tunnel. A panicked woman is swept away to her death. The tunnel ends at a waterfall plunging into a chasm, but they spot a ladder leading to a hole in the ceiling; however, it is just out of reach.

Pendergast informs Margo that the creature killed the SWAT team and Wright, and that Coffey has withdrawn all personnel and refuses contact. The rising floodwaters are impassable, giving D’Agosta only marginal survival chances. Pendergast proposes that Margo and Frock wait in the secure area while he hunts the creature alone. Margo refuses, and Frock persuades Pendergast to take her along. Margo locks Frock inside the secure area, taking his keys and the fiber bundle.

Smithback proposes making a rope from belts to loop over the ladder. Smithback successfully tosses the improvised rope over the lowest rung, and they wait for the rising floodwaters to lift them high enough to reach it.

Pendergast and Margo follow the blood trail to the first floor. Margo proposes that they act as bait, making noise to lure the creature. They move toward the long corridor Frock identified, only to find a steel security door bisecting it, reducing their firing range to an insufficient 125 feet; they have no choice but to proceed with the plan.

In the command unit, Coffey grows increasingly paranoid, blaming Pendergast, D’Agosta, and others for the crisis. Over the radio, he refuses to send help to Garcia and tells them that they must wait for power restoration.

Inside security command, Garcia, Allen, Waters, and two others smell the creature’s stench as it begins battering their door. Garcia again radios Coffey for help. Pendergast and Margo hear the attack from around the corner. Margo warns that the creature may understand English, so they shout, pretending to be lost in order to draw the creature away from security command. Pendergast kneels and aims his pistol, instructing Margo to activate the miner’s light on his signal.

Meanwhile, Waters panics and abandons his post, leaving Garcia alone. An Agent Slade has replaced an indisposed Coffey as commander and tells Garcia that he cannot send a team to help.

The rising water lifts D’Agosta’s group toward the ladder. Finally, they climb up the ladder into a horizontal pipe opening into a dark, foul-smelling chamber; Smithback helps the others through just as D’Agosta’s flashlight dies. One survivor briefly illuminates the space with a lighter before dropping the tool in shock.

The creature charges down the corridor toward Pendergast and Margo. At Pendergast’s signal, Margo activates the miner’s light, and the agent opens fire. He strikes the creature’s head, its right foreleg, and its left hind leg, but it barely slows. With the creature closing rapidly and only one bullet remaining, Margo believes their plan has failed.

In security command, Garcia and the others hear the gunfire, then silence—followed by a rattling at their door. Garcia assumes the creature has returned.

D’Agosta relights the lighter to reveal a chamber filled with animal and human bones—the creature’s “larder.” Decapitated human corpses hang from metal supports along one wall. Smithback recognizes George Moriarty’s watch on one of the bodies. D’Agosta finds an upward-sloping passage and leads the group to a ladder beneath a locked manhole. He yells for help, and people on the street above agree to call the fire department in exchange for $50. D’Agosta announces they are saved.

The rattling at security command proves to be Pendergast knocking. Garcia opens the door to find Pendergast and Margo alive but covered in the creature’s blood. Pendergast credits Margo with the kill; in the final moment, she realized the creature’s forward-facing primate eyes offered a direct path to the brain and told Pendergast where to aim. His last bullet entered the eye and destroyed the brain instantly. As Margo goes into shock, Pendergast says they must rescue Frock and send relief for D’Agosta. Garcia informs him that Slade is now in command, and Pendergast expresses relief that he does not have to speak with Coffey.

Four weeks later, Margo joins Frock, Pendergast, and D’Agosta in Frock’s office. Frock laments that the government confiscated the creature’s corpse, preventing study. He explains the creature combined reptile and primate traits, and that the Mbwun plant is believed extinct; its native habitat was destroyed, and the FBI incinerated all museum specimens. Smithback arrives with a book contract and announces his plan to donate half his royalties to Officer Bailey’s family. Pendergast reveals that D’Agosta has been promoted to captain. He then identifies five of the eight bodies from the creature’s lair, including Moriarty and the long-missing employee, Montague. He explains that Wright, Rickman, Cuthbert, and possibly Ippolito had suspected for years that a creature was in the museum. Moving the Whittlesey crates blocked the creature’s access to the plants and inadvertently triggered the killings. Frock notes that Wright and Rickman are dead and Cuthbert is now in a mental institution; he theorizes the creature was drawn to the exhibition by the Mbwun figurine—its only link to home.

Pendergast reveals that the killings began in a warehouse in Belém, Brazil; he theorizes that the creature killed Whittlesey, given that a piece of the man’s medallion was found in the lair. Coffey has been reassigned to Waco, and Pendergast may become director of the New York FBI office. Margo has accepted a tenure-track professorship at Columbia. The group toasts their futures and Moriarty’s memory.

Six months later, Gregory Kawakita works in a secret warehouse laboratory in Queens, cultivating plants and running his extrapolator program on a hacked medical mainframe. He reflects that he alone discovered the truth of the science behind the Mbwun creature. After reviewing Margo and Frock’s analysis of the reovirus, he took a single Mbwun fiber from Margo’s handbag, successfully cultivated the plant, and inoculated it with its ancient reovirus. Kawakita’s thoughts reveal that the Mbwun creature was actually Whittlesey, who had been transformed by the reovirus. The Kothoga had force-fed him the plant to create a controllable creature—and then had failed to control it. Kawakita believes that he will succeed in a similar endeavor because he now controls the only source of the plant that the Mbwun creature needs.

He sells the plant’s narcotic effects as a street drug called “glaze” to fund his research. He notes that, with the effects of the drug, his own senses are sharpening and his allergies have disappeared. He reflects that he could win a Nobel Prize—but he has grander plans. Another customer knocks on his door.