Mikado, a young man longing for something unusual in his life, moves to Ikebukuro at the invitation of his childhood friend Masaomi. Arriving in Tokyo, he begins his new life as a high school student, awed and mesmerized by the new world around him.

It is the Entrance Ceremony at Raira Academy, and the auditorium swells with a varied mix of emotions emitted from the students. Amidst all this is Rio Kamichika: a girl with a notably dark vibe following her.

Masaomi Kida is out about town, fervently trying to pick up girls, while Mikado tags along, feeling a bit confused and bewildered. Various people intermingle throughout Ikebukuro as rumors of the “Dollars” spread.

People throughout the city speak of an urban legend known as the “Headless Rider”. A surprising number of people have personally witnessed it speeding down the streets on a jet-black motorbike with no license plate.

While hanging out with Anri, Mikado and Kida learn about her worries for her missing friend and try to cheer her up. Later the duo gets themselves in trouble when they are cornered by a gang of thugs.

The Dollars gang figures that a foreigner friend of theirs was captured by the manhunters and search through Ikebukuro determined to rescue him.

Shizuo Heiwajima, also known as “the strongest man in Ikebukuro”, is a man who definitely relishes that title. Though he carries with him a high esteem, something is amiss. Lately he has been extremely short-tempered and does not know why.

Celty runs away from home after arguing with Shinra, and an exchange student asks people to write what they're looking for in a notebook she carries.

After losing contact with her brother Seiji, Namie Yagiri enlists Izaya's help to find him. While roaming through Ikebukuro, Seiji and Mika Harima stumble onto Shizuo and Celty and a heated pursuit begins after Celty figures that the head attached to Mika's body is actually hers.

Mikado runs away with Mika and shelters her into his apartment. However, in the following day, he is approached by Celty and Izaya, and after telling her secret to him, Celty convinces Mikado to help her find Mika. Unfortunately, Mikado is cornered by some Yagiri Pharmacy workers who question him on Mika's whereabouts. In order to save Mika, Mikado reveals to Izaya and Celty his secret.

Anri's missing friend, the Dullahan, the girl with the scar on her neck, Yagiri Pharmaceuticals, the kidnappings, and the Dollars... little by little, the pieces begin to fall into place.

It is discovered that Harima Mika is actually alive, and that Celty's head is being held by Yagiri Pharmacy. Shinra had known about it, and kept the secret from Celty for the fear of losing her because of her head's will.

Half a year has passed since the Dollars meeting and Ikebukuro seems to have returned to normal. But underground, the Yellow Scarves and the Slasher are becoming increasingly active. Darkness approaches, ready to destroy the days of peace.

Anri is attacked by the Slasher. The same night, the user Saika appears in the chatroom, and posts a puzzling message. Mikado, worried about rumors that the Slashers are the Dollars, decides to cooperate with Celty.

Magazine Journalist Shuji Niekawa’s unbridled passion is raging. A Russian who runs a sushi shop, the Awakusu organization, an Information Broker, the Headless Rider... He investigates the supposedly strongest man in Ikebukuro: Shizuo Heiwajima.

Anri is targeted by the Slasher, but Kyohei’s gang moves to rescue her. Shizuo and Celty join in, and after defeating the Slasher, reveal his true identity. However, this moment of relief doesn’t last as Celty reads what has been posted in the chatroom.

Civil unrest begins to descend upon Ikebukuro. Masaomi finds himself in an abandoned building, depressed, thinking about his past: how he ended up back there, and how a girl still waits for him at a hospital.

Anri notices something is wrong with Masaomi, and takes action to find out what it is. Elsewhere, a gang-war breaks out between the Yellow Scarves and the Dollars over the Slasher’s identity. The standoff grows as Mikado’s desire to stop it is ignored.

After doing some investigating, Masaomi starts to suspect that the remnants of the Blue Squares, a gang that he once fought, have slipped into the Dollars. He decides to visit Kyohei’s gang to learn the truth.

Despite Mikado’s orders, the Yellow Scarves hunt down members of the Dollars. Mikado begins to question whether the existence of the Dollars is worth such a sacrifice. Anri tries to put a stop to the gang war, but ends up making the situation worse...

The Dollars are enraged at the Yellow Scarves’ actions. The Yellow Scarves learn that Anri is the girl who escaped from their hideout during the night of the meeting, and track her down. However, an unexpected group of people steps in to save her...

A gunshot resounds from an alley, echoed by a phone call for Masaomi. Mikado rides with Celty, and Anri learns the truth. Their hearts are filled with trust, doubt, and unease. Everything rushes toward a conclusion, and Izaya enjoys the chaos.

Filled with unwavering determination, Masaomi enters the abandoned factory, and encounters the unexpected. At last: Masaomi, Mikado, and Anri face off. Although each of them carries inexpressible feelings, they eventually find an answer...