In the aftermath of the 2014 San Francisco attack, an event now known as G-Day, schoolteacher Cate Randa travels to Tokyo to settle the affairs of her father, Hiroshi, who has been declared dead. Upon arrival, she discovers that her father led a double life, leaving behind a second family including a half-brother she never knew existed, the artist Kentaro, and his tech-savvy ex-girlfriend, May. Together, the estranged siblings uncover evidence that their father was not merely a businessman but a scientist deeply embedded in Monarch, the secretive organization tasked with tracking and studying massive unidentified terrestrial organisms known as Titans.

Their investigation puts them on the radar of Monarch and leads them to a crucial link to the past: Army officer Lee Shaw. In the present day, Shaw is portrayed by Kurt Russell as a weathered figure with decades of secrets, while flashbacks to the 1950s feature Wyatt Russell as the young military man assigned to a clandestine project. These historical sequences reveal the origins of Monarch, following young Shaw as he works alongside determined paleobiologist Dr. Keiko Miura and her ambitious colleague Bill Randa. In this era, the trio witnesses the emergence of Godzilla in the South Pacific and struggles to convince skeptical government officials that Titans are real, fighting to get the organization off the ground while navigating personal entanglements and bureaucratic interference.

As Cate, Kentaro, and May chase clues across the globe while being pursued by Monarch agents, they learn that Hiroshi faked his death to continue his research into Hollow Earth—a theorized realm beneath the planet's crust where Titans originate. The narrative builds toward a climactic journey into this subterranean world, where the group discovers that time flows differently. There, they find a shocking survivor: Keiko Miura, who fell into Hollow Earth in 1959 and has aged only weeks while nearly six decades passed on the surface. The family reunion between the unaged Keiko and her now-elderly son Hiroshi forms an emotional core of the story.

During the escape from Hollow Earth, Lee Shaw sacrifices himself to ensure the vehicle carrying Keiko, Cate, and the others can return to the surface. However, upon emerging, the group discovers that what felt like days in Hollow Earth amounted to two years in the outside world, advancing the timeline to 2017. They also learn that Kentaro and Hiroshi have aligned with Apex Cybernetics, a powerful corporation destined to play a pivotal role in future Titan conflicts. The season concludes on Kong's Skull Island, where King Kong himself emerges, setting the stage for the escalating confrontation between humanity and the Titans.

Season two picks up immediately from this moment, with Cate determined to rescue Shaw, who survived his fall and remains trapped in the interdimensional space of Axis Mundi. The rescue operation inadvertently releases a new, squid-like creature designated Titan X into the world, sparking a fresh global race between Monarch and Apex to either contain or exploit the ancient being. The season further explores the complicated history between Keiko, Shaw, and Bill Randa, revealing past secrets that ripple through the family in the present day. New characters enter the fray, including Isabel, a persuasive businesswoman with deep ties to Apex, as the series continues to weave together past and present while expanding the mythology of the MonsterVerse.