In 1999, 45 years after the original Godzilla’s attack,[a] maser-cannon technician Lieutenant Akane Yashiro is unable to kill a new member of Godzilla’s species during her first fight and accidentally knocks a vehicle down the mountain, where it and its occupants are crushed by Godzilla. As a result, Akane is demoted while scientists, including single father Tokumitsu Yuhara, are gathered to build a bio-mechanical robot from the original Godzilla’s skeleton. The cyborg Mechagodzilla, nicknamed Kiryu, is finished and inducted into the Japan Self-Defense Forces along with its human pilots, the Kiryu Squadron, with Akane becoming the primary pilot. However, memories of Akane’s actions during the original fight still linger, and one of her squadron mates, Second Lieutenant Susumu Hayama, holds her responsible for the death of his brother.

Four years later, Kiryu is unveiled in a global presentation where its remote systems, use of command aircraft, and Absolute Zero Cannon are shown. Simultaneously, Godzilla returns, and Kiryu is launched into battle. In the midst of this however, Godzilla’s roar causes Kiryu to experience memories of the original Godzilla’s death and destroy the city while Godzilla retreats. The horrified Kiryu Squadron are powerless to stop the rampaging cyborg until it runs out of energy and is brought back to headquarters for repairs.

Meanwhile, Akane deals with Hayama’s attempts to make her leave and Tokumitsu’s attempts to get to know her despite her desiring solitude. Later, Godzilla attacks again. Once the repairs are completed, Kiryu is deployed and confronts Godzilla once more. Kiryu gains the upper hand, but as it prepares the Absolute Zero Cannon, Godzilla fires its atomic breath, knocking the cyborg away and diverting the blast. With Kiryu disabled and the remote piloting system taken off-line, Akane orders Hayama to land his command craft so that she can use Kiryu’s internal backup cockpit.

Before she leaves, Hayama wishes her luck, forgiving her. Piloting Kiryu directly, Akane closes in on Godzilla, hoping to use the Absolute Zero Cannon at point-blank range. The two monsters collide, and Akane uses Kiryu’s thrusters to propel them out to sea before firing. In the aftermath, a living yet scarred Godzilla retreats once more while Kiryu is heavily damaged. With the Kiryu Squadron successful in repelling Godzilla, Kiryu is taken back to base for repairs. In a post-credits scene, Akane agrees to have dinner with Tokumitsu and his daughter Sara and salutes Kiryu.