In 2035, ten years after the Battle of the Breach, former Jaeger pilot Jake Pentecost – son of Stacker Pentecost – makes a living by stealing and selling Jaeger parts on the black market in the Los Angeles area. After he tracks part of a disabled Jaeger’s power core to the secret workshop of fifteen year-old Jaeger enthusiast Amara Namani, both are arrested by the Pan-Pacific Defense Corps after an altercation between Amara’s small, single-pilot Jaeger Scrapper and the Jaeger November Ajax. Jake’s adoptive sister and PPDC Secretary General Mako Mori gives Jake a choice between the prison or return to PPDC as an instructor with Amara as his recruit.
Upon arriving at a Shatterdome in China, Jake starts training Jaeger program cadets with his estranged former co-pilot Nate Lambert. Nate and Mako reveal to him that the Jaeger program is threatened by Shao Corporation’s drone program, which offers to mass-produce Jaeger drones developed by Liwen Shao and Dr. Newton Geiszler. Mako is due to deliver a final assessment to determine the authorization of the drones at a PPDC council meeting in Sydney, but is killed by rogue Jaeger Obsidian Fury before she can report. Her death prompts the PPDC council to authorize the drone program and order their immediate deployment. Moments before her death, Mako transmitted the location of a defunct Jaeger production facility in Siberia before Jake failed to save her. Jake and Nate travel to the area in their own Jaeger, but Obsidian Fury destroys the complex and engages them in battle. Upon destroying its reactor, they find that Obsidian Fury was controlled by a Kaiju’s secondary brain, which testing shows was grown on Earth.
When the drones reach their respective locations, they are taken over by cloned Kaiju brains and simultaneously attack Shatterdomes worldwide, inflicting heavy casualties on the PPDC forces and incapacitating almost all Jaegers. Hermann Gottlieb seeks out Geiszler for help, only to discover that Geiszler is the mastermind behind the attack. Geiszler’s mind has been taken over by the Precursors, the alien race who created the Kaiju, due to his regularly drifting with Kaiju brains. Seeking to destroy the world for the Precursors, Geiszler, now their emissary, commands the Kaiju-Jaeger hybrids to open new breaches all over the world. Although Shao is able to destroy the drones, three powerful Kaijus named Raijin, Hakuja, and Shrikethorn – emerge from the breaches and unite in Tokyo. The team realizes that the Precursors’ goal is to activate the Ring of Fire by detonating Mount Fuji with the Kaiju’s chemically reactive blood, spreading toxic gas into the atmosphere and wiping out all life on Earth, terraforming the planet for Precursor colonization.
The cadets are mobilized while Gottlieb and Shao repair the PPDC’s four remaining Jaegers; Gottlieb invents Kaiju-blood-powered rockets, which launch the team to Tokyo. Although the Jaegers initially repel the three Kaiju, the Precursor Emissary merges them into a Mega-Kaiju that quickly overpowers the Jaegers, injures Nate, kills Suresh and destroys three of the four Jaegers leaving Gipsy Avenger as the only operational Jaeger. Jake and Amara pilot it against the Mega-Kaiju, with Shao remote piloting Scrapper and aiding them by locating a rocket and welding it to Gipsy’s right hand and sending the Jaeger into orbit and allowing to freefall back to earth, colliding into the Mega-Kaiju which kills the Kaiju as Jake and Amara survive by transferring into Scrapper. Afterwards, Nate takes the Precursor Emissary into custody.
Some time later, the captive Precursor Emissary threatens that Precursors will attack the world over and over again. Jake replies that next time, humanity will be the ones attacking the Precursors.