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In 2014, following Godzilla's battle with theMUTOs inSan Francisco,^[a] schoolteacher Cate Randa reunites with her estranged father, Hiroshi, who then leaves without elaboration. He later disappears in Alaska and is presumed dead. In 2015, Cate travels toTokyo to settle Hiroshi's affairs. She discovers that he had a second wife, Emiko, and a son, Kentaro, in Japan. Kentaro leads Cate to Hiroshi's office, where she discovers a safe containing files belonging to their grandfather, Monarch researcher Bill Randa. Seeking answers about Monarch's presence in San Francisco and Hiroshi's connection to them, Cate and Kentaro recruit Kentaro's ex-girlfriend May Olowe-Hewitt to decode the files. Monarch employee Tim is notified of their activity.

In 2015, Kentaro discovers Monarch files in Hiroshi's office indicating that Shaw, his honorary great-uncle, moved to an assisted living facility in Japan. Tim and Monarch field operative Michelle Duvall track down Cate, Kentaro, and May in an attempt to find the decoded files, but they escape. Cate, Kentaro, and May go on the run and find Shaw, who reveals that the facility is a pretense for Monarch to keep him under house arrest. Shaw convinces them to escape from the facility and follow Hiroshi to his last known location in Alaska.

In 2015, Cate, Kentaro, May, and Shaw escape Japan on a ferry bound for Pohang, Korea. In Pohang, they are accosted by border guards before one of them, Du-Ho, reveals himself as Shaw's old friend. Du-Ho transports them to Alaska by plane; on the way, May infers from Bill's files that Hiroshi was likely following a list of coordinates identified by Monarch. In Alaska, they find the wreckage of Hiroshi's plane as well as an encampment suggesting his survival. Du-Ho realizes that Hiroshi's plane was attacked after landing; a Frost Vark kills him and destroys his plane.

In 2015, the Frost Vark's emergence is detected by Monarch. Cate, Kentaro, May, and Shaw manage to escape from the Frost Vark, but May falls into a pool of water and quickly develops hypothermia as they try to find shelter. Kentaro splits off from the rest of the group and finds a building that he saw from the plane, which turns out to be an old radio station that had previously been repaired by Hiroshi. Having learned that the Frost Vark feeds on heat energy, Cate, May and Shaw create a bonfire to distract it, long enough for a helicopter that Kentaro contacted to arrive and rescue them. The group are taken to a Monarch outpost, where they are greeted by Tim and Duvall.

In 2015, Monarch deputy director Natalia Verdugo is frustrated to learn that Shaw has kept Cate, Kentaro, and May in the dark about Hiroshi's activities in Alaska. Duvall suggests releasing the three to track their movements. After returning to San Francisco, Cate convinces her mother, Caroline, and Caroline's colleague James to smuggle them towards Hiroshi's office in a restricted zone of the city's ruins. Evading military patrols and dealing with Cate's PTSD, they eventually reach Hiroshi's office. While they fail to find further hidden files, Kentaro concludes from Hiroshi's maps that he likely headed to Africa in search of Titans. May secretly contacts Duvall, asking to go home in exchange for her cooperation.

In 2015, Duvall breaks Shaw out of captivity, revealing that she joined Monarch after her sister died in the Janjira power plant disaster^[a] but has become disillusioned. They take Cate, Kentaro, and May to the Algerian Sahara, where they find Hiroshi using a Titan lure. He warns them to escape before fleeing. Tim arrives with a team of Monarch agents, but Godzilla emerges, having been sleeping underground, and causes their helicopter to crash. Shaw and Duvall reveal their intent to follow and help Godzilla, but Cate, Kentaro, and May leave to find Hiroshi. Cate and Kentaro are angered when May reveals that she allowed Monarch to track them.

In 2015, May is kidnapped at the airport in Tindouf, Algeria by her former employer, Brenda Holland of Applied Experimental Technologies, who gives her the choice of spying on Monarch or being prosecuted. Cate accosts Tim when he arrives at the airport and asks him to help locate May. Tim, Cate, and Kentaro find May's family in Tacoma, Washington and learn about her past from her sister, Lyra Mateo. They trigger a false Titan alert to rescue May from AET, but she chooses to stay behind and not spy on Monarch. Verdugo is convinced by Cate to secure May's release in exchange for help understanding Shaw's plans, and by Tim to take Monarch public to explain the alert. After reaching an agreement with Monarch, AET rebrands to Apex Cybernetics.^[c] Shaw and Duvall take over the Alaskan Monarch outpost and detonate a rift to the Hollow Earth to seal it.

In 2015, Shaw and Duvall return to the Kazakh power plant where Keiko was lost in 1959, now enclosed in a containment facility. Cate, Kentaro, May, and Tim infer that Shaw is trying to rectify the past. Verdugo sends them after Shaw with a small team. Inside, Shaw and Duvall confront the team. Speaking with Cate alone, Shaw explains that he intends to help Godzilla maintain order by separating theHollow Earth from the surface world. As Shaw primes explosive charges around a rift to the Hollow Earth inside the pit, an adult Endoswarmer emerges. May, Cate, Shaw, and the Endoswarmer fall back into the rift before its destruction.

In 2015, Monarch rescues Kentaro and Tim. Verdugo informs a despondent Kentaro of Cate, May, and Shaw's losses. Kentaro's mother, Emiko, inspires him to continue searching. When Hiroshi returns to his office, Kentaro confronts him. Meanwhile, Shaw and May awaken in an intermediate realm between the surface and the Hollow Earth, Axis Mundi, and search for Cate. Elsewhere, Cate is attacked by a Bramble Boar but is rescued by an unaged Keiko.

In 1962, Shaw volunteers to lead Operation Hourglass, an expedition into the Hollow Earth. Suzuki's Titan lure is used to induce a partial Titan emergence and stabilize a rift. During the launch, the rift destabilizes and closes, and Shaw’s team is lost. Monarch's funding is cut due to this incident. Meanwhile, an Ion Dragon kills Shaw's team while he is sucked back through the rift.

In 2015, Keiko explains to Cate that she rigged the Titan lure from Operation Hourglass to send a distress signal from theHollow Earth. They reunite with May and Shaw; Keiko is devastated to learn that decades have passed and Bill died on his expedition to Skull Island.^[b] Tim leaves Monarch after clashing with Verdugo over her refusal to investigate Keiko's signal, and instead informs Kentaro and Hiroshi. As Shaw and Keiko reconnect the lure to the Operation Hourglass launch vehicle, she reveals her intention to remain behind, but Cate persuades her otherwise. Shaw activates the vehicle, but inadvertently lures an Ion Dragon already present in Axis Mundi. Shaw exits the vehicle to reconnect a cable dislodged by the Dragon. Godzilla emerges through a rift and battles the Dragon, eventually throwing it back through the rift and activating the vehicle. As Keiko struggles to bring Shaw back into the vehicle, he sacrifices himself to allow their escape.