Construction of an artificial island is disrupted by an unexplained phenomenon known as "burning sea". Masamichi Haru is injured by burning sea during a test of early Meta-Real technology, leaving him comatose for fifty years. Now elderly and wheelchair-bound, he still hopes to solve the mystery of burning sea. His friend Eichiro Kushima now hopes to use the Meta-Real, also known as the Metal, to research the burning sea phenomenon.

Haru has become an official investigator and is asked to dive into the Metal to rescue the consciousness of an Artificial Island shareholder who has experienced braindown.

Minamo and Sota investigate reports of ghost sightings at Minamo's school.

Holon collapses, and the others attempt to complete their investigation without her help.

After the spread of weather particles, drastic weather changes occur across the planet, and the burning sea phenomenon returns. Haru decides to use the experimental deep dive suit in an attempt to make contact with Kushima.

Haru makes contact with Eliza and receives Kushima's proof that the weather particles will cause worldwide disaster. Haru broadcasts the proof on the Metal, and the world's leaders quickly agree to shut down the Metal to kill the weather particle nanomachines. Kushima's consciousness then contacts Haru and explains that the ocean itself will replace the functionality of Metal via the salt water in the human body. Haru, restored to his younger self, is safely returned to the surface, where he reunites with Minamo.