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.

Aoi Minamo is hired to be Haru's assistant. When burning sea causes a power outage that threatens life support systems on the artificial island, Minamo rushes to the electrical substation, while Haru uses his cyberbrain to dive into the Metal Network.

Haru struggles to become proficient enough at Metal diving to help Kushima's research. During his final test, he experiences braindown.

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's father shuts down the core server to minimize damage from a virus intrusion, putting his job on the line.

Minamo goes for a dive in the sea. This episode is a recap of the series so far.

Following the success of weather particle experimentation, the Secretary-General and Jeni En want to install weather particle plants as soon as possible. Kushima is opposed to the plan, suspecting that the weather particles will cause complications that threaten the Artificial Island. Meanwhile, Sota goes on a date with Holon.

Kushima goes missing, and is later found without his cyberbrain. Brain death will occur within twelve hours, so Sota and Holon search for his cyberbrain while Haru searches the Metal for his consciousness. Meanwhile, with Kushima missing from the Trustee meeting, the Secretary-General has no choice but to approve Jeni En's motion to begin bringing the weather particle plants online.

With help from the Secretary-General, Sota deciphers the clues to bringing Kushima's cyberbrain back online, but instead of Kushima, an emergency AI awakens. The AI explains Kushima's suspicion that the weather particles cause the burning sea phenomenon, convincing the Secretary-General to halt weather particle production until Kushima can prove his theory. However, Jeni En temporarily revokes the Secretary-General's authority with a vote of no confidence.

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.