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.

Because of her lack of a cyberbrain to read online texts, Minamo must find a physical book for a book report. Her discovery reveals the true story of a lost love.

Minamo and Haru discover a dog whose consciousness was swapped with that of his owner. They hurry to find the owner's body before it becomes too late for them to switch them back.

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

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

Those who contact a mysterious oracle in the Metal named Eliza end up with lost memories. During the investigation, Minamo realizes that Haru has been talking to none other than Eliza.

Minamo tries to help violinist Ichinose, who has been discouraged ever since Kushima suddenly quit playing violin long ago.

Minamo meets Amy, a girl who has just received cybernetic eyes to cure her blindness, but learns that Amy is struggling to adjust to being able to see. Meanwhile, Haru is asked to investigate the disappearance of a highly sought-after artist in the Metal.

Haru reminisces about his youth, from his parents' struggles with poverty that led to trouble with the yakuza, to his meeting a dolphin that inspired his fascination with the sea, and finally to his exploration of the ruins of his city, now underwater because of climate change, which led him to become a test diver for early Meta-Real experiments.

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

Haru investigates cyberbrain deterioration in a group of food connoisseurs.

Sota tries to train enough to defeat Holon in battle. Meanwhile, Haru investigates a case of a female android being illegally used for prostitution.

Minamo's family comes to visit.

Haru, Minamo, Sota, and Holon go to a distant jungle island to investigate a mysterious background noise in the Metal. All seems well until ionization in the rainforest disrupts Holon's cyberbrain.

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

At the jungle island, Haru realized that he can learn to walk again, and he begins to practice in secret to avoid jeopardizing his job as a Metal diver. Meanwhile, Minamo gets tested for suitability to receive a cyberbrain.

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.

Sota breaks into the weather particle facility with help from Haru in the Metal, but before he can reach the control room where the weather particle launch can be halted, Sota must fight Jeni En.

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.