Berry is a girl living in the data-managed city of Tom Sawyer Island. Her hobby at the moment is trying to catch Phantom Zero, who's believed to be behind the cases of Love loss known as the Zero Phenomenon. One day, when she heads into town to get the broken Deco in one of her eyes fixed, Berry runs into a kid who seems like a ghost, due to being unable to be seen with Deco. Suspecting she may have finally found the Phantom, Berry begins her chase.

Berry and Hack are somehow able to escape from the Hyperverse that Phantom Zero pulled them into. But before long, Hack is apprehended by the customer center, who are investigating the Zero Phenomenon. The next day, Berry wakes up on the veranda of her apartment, and after trying to explain what happened, her friends point out to her that there is no evidence of Zero Phenomenon having occurred, much less of the kid she encountered. Not taking no for an answer, Berry decides to dig up proof behind the Zero Phenomenon.

Hack is being held at the customer center under suspicion of being Phantom Zero, where she's questioned about the crime of forcibly erasing Love. Meanwhile, Berry learns from the mysterious Finn about how he and his comrades are ghosts, citizens who live in the city despite not being registered. Finn is skeptical that a fellow ghost would have helped Berry, and obtains the data on Phantom Zero from the paper plane device of Hack's that Berry brought.

Four months have passed since the trial. Berry is now a ghost herself, and has joined the detective club alongside Hack and her friends. They're trying to capture Phantom Zero, and discover the truth behind the Zero Phenomenon. And that's when a certain client approaches them. This man wants them to find his missing daughter. But after a bit of digging, it turns out the missing girl isn't his daughter, but the female avatar that he had been using. Not only that, but the timing of the disappearance seems to have something to do with when Berry and Hack were caught in a Zero Phenomenon incident.

The Ghost Detective Club has a new case. The client is a professor that uses Deco overlays to create artificial animal that he has on display at his Neo Animal Museum. His self-proclaimed masterpiece, the Nue, has an appearance that doesn't match the listing on Decopeedia, and hires the detective club hoping to clear up the confusion. After getting a glimpse at the professor's Nue, it looks nothing like the cute creature whose picture is on the Decopedia page. Even so, the professor insists that his Nue is the accurate version.

A new client has arrived. This time it's an AI drone, named Doron, that Smiley dug out of a garbage pile. With it's memory missing, it asks the club to find it's missing owner. After examining Doron, it becomes apparent that Doron is an illegal drone that isn't registered with the customer center. And on top of that, the only camera data still in their files appears to be of an avatar that is fighting against Phantom Zero.

Berry catches wind of a ramen cart that nobody knows the location of. In order to find it, Watson begins checking rumors from all across the island. Berry suggests that the detective club search for the cart, but the other members aren't interested. As Berry and Watson investigate the rumors, Watson receives a tip on the location of the cart. In pursuit of ramen, Hack, Berry, and Watson set out to find it.

Berry is helping Hank sort through the junk that he has salvaged at the harbor when they encounter an old friend of Hank's, named Will, who informs them about an older model of satellite that's expected to crash down into the nearby sea. Back at the agency, the peacock feather-like circuit that Watson received from Analytica is being analyzed. When Hank returns, he insists that they all head to the area Will tipped them off about.

When Finn was young, his family lived in a slum where garbage tended to be dumped. One day, his brother brings him an older model of Deco that should be easier for Finn to use due to his Deco-Sickness. With it, Finn accidentally discovers that the local purification systems are broken. Believing this is what has caused his home to become polluted, he uses the Deco that he got from his brother to request that the customer center fix the purification system. But because he isn't registered as a citizen, his login is flagged as illegal, which leads to his request not being answered.

After being suspected of being Phantom Zero, Berry and the club use Deco disguises in order to escape. Meanwhile, the customer center is in a frenzy, thanks to reports of Phantom Zero that they're receiving from all over the place. They dispatch a search team to the slums. Finn and the detective club take shelter in one of Finn's secret hideouts, with Finn stating the only way they can clear their names is to head to the mysterious location known as Mark Twain, and apprehend the true Phantom Zero.

Thanks to Doron and his drone friends, Berry, Hack, and Finn are able to reach Mark Twain, a strange facility floating in the sky. By using the Angelfish club card they had previously obtained, they manage to get inside, where Berry and Hack enter Mark Twain's rendition of the Hyperverse. What they discover appears to be a labyrinth. Knowing that all the secrets of Tom Sawyer island must be contained within, Berry and Hack start searching for Phantom Zero's identity.

A young girl awakens in a empty white space. She's enjoying a happy life with her parents, staring out at her pet peacock. But then, from out of nowhere, Berry appears. The girl is surprised, and attempts to run away.