In the year 2012, the ambitious project for a city built on an artificial offshore island collapsed in the middle of construction due to a phenomenon called "burning sea." Sea diver Masamichi Haru, who accidentally encountered the phenomenon while conducting observations in the nearby sea area, has remained in state of suspended animation since the incident. When he wakes up, he finds himself in the year 2061. Although he is physically an old man even unable to walk, his mind seems to have remained the same as of the day of the incident. But the world around him has undergone great changes, too. And in the year 2061, Eichiro Kushima, Haru's friend before the incident and now the managing director at the Electronics Industry Physical and Chemical Research Institute, is observing the same burning sea phenomenon, that once collapsed the artificial island. But Kushima's place of observation is within the higher-order information space called Meta-Real Network or, more commonly, Metal.

The artificial island is severely hit by the burning sea phenomenon and by a following unidentified impact wave. The violent impact causes a power outage on the entire island and the life-support devices in the hospital have stopped operating. In order to resolve the crisis, Haru's young assistant Minamo runs on the abandoned monorail track heading toward the electrical substation. Meanwhile, Haru plunges into the Meta-Real Network. Inside this new environment, he feels a new "sea," and begins to utilize his ability to a completely different kind of diving, this time inside the human brain.

Haru witnesses the fifty-year history of the artificial island created by Eichiro Kushima. After he saw the new "sea" in the Meta-Real Network, he decides to take the "brain dive" test conducted by Kushima so that he would feel the sea again. But Haru is too dominated by the anxiety of loosing the sea again, and the test turns into disaster just because of his persistence. What is required of a "diver"? Haru learns the answer to this question through Minamo, but as he tries to take the final test, "braindown" occurs.

The first client to visit the Masamichi Haru Investigation Office was Jenny En from the Advisory Commission. With Kushima's introduction, Jenny has come to ask Haru if he can rescue one of shareholder of the artificial island, who went through braindown. Jenny want Haru to investigate the cause of the braindown, and recover his consciousness. Although it is a difficult request, Haru agrees to take on the job. Minamo is chosen as his buddy and she begins to see what she can do.

Minamo's elder brother, Sota Aoi frequents a practical fighting community within the Meta-Real Network and tries to improve his skills. He goes to see the android Holon to find the reason for his loss. At the same time, Minamo is looking for a pair of sunglasses by Sous-Marin brand, which used to be trendy items among divers decades before, and are now considered rare pieces for collectors. She hopes to give the pair to Haru for the opening of his office. This type of shades is also a trademark of Iron Schwartz, the undefeated champion of the practical fighting community. But while Minamo is looking for a Sous-Marin, a scream echoes on the island...

15-year-old Minamo has to write a book report for homework. But as all the books on the artificial island are on electronic support, Minamo cannot read them because her brain is not cyber-interfaced. At last, she finds a real printed volume that seems to suit for her report in a small collection inside the Central Library. But as she reads through the pages, she realizes the hidden sentiment of the person who used to own the book. The feelings for a lost love...

Masamichi Haru Investigation Office has a new client. His name is Dapoo. In fact, he walks on four legs, and nobody would hesitate in describing this hairy "client" as a dog. Moreover, the animal looks exactly like a dog in a popular kids' TV program Minamo used to watch in Australia. She realizes Dapoo wants to communicate something desperately. As Haru accesses Dapoo through the Meta-Real Network, he finds that Dapoo's and his owner's consciousness were swapped. But then, where is the body of the owner?

A strange rumor is spreading on the artificial island: people are reporting of a mysterious girl that nobody knows or has ever seen before. Sota begins to investigate. Meanwhile at Minamo’s school, students start to tell scary stories about a ghost appearing in the building. During a swimming lesson, Sayaka saw a mysterious girl who drifted in water. And when Yukino went back to the school to pick-up something she forgot to take home, her arm was seized by a white hand in a supposedly empty hallway. Who is the ghost? As Sota arrives on the spot, they all start with the “ghost hunting.”

Minamo and Sota's father, Mamoru Aoi, is the chief of the Technical Section in the Department of Management at Denriken. He always puts his work first and though has not been a good father at home, he is a capable and popular supervisor at work. One day, there is a system intervention in the Metal at Denriken. A virus intrusion is suspected and Mamoru shuts down the core server to minimize the damage. This consequently minimized the effect of the disabled system, but his effort brought Kushima under fire for his managerial responsibility at a special meeting of the board of trustees.

At Minamo's school, girls talk about a reputed medium in the Metal. Her responses seemed as if she foresees everything, and this captured her fervent followers. Her name is Elisa. However, it became apparent that humans who got in touch with her had a part of their memory lost, thus DenRiken initiates an investigation to find the identity of the mysterious medium. At the same time, Haru is chatting on the Metal in his office. And his interlocutor introduces herself with the name of... Elisa!