Maeda Yoshiaki has been falsely accused of murder and sent to the Shouran Academy Juvinile Detention Center. There he meets Cell Four inmates Yoshioka Masafumi, Yamanoi Mitsuru and Iwakura Gou. Suddenly a virus that makes people violent and cannibalistic spreads throughout the Academy. The boys take the academy's only vehicle and go to Maeda's home to find his family are all infected. While grieving and planning what to do next a mountain of bodies with a naked man on top of it approaches them.
- Chapter 4 - Whole Lotta Despair
- Chapter 5 - Bitter Fix
- Chapter 6 - Heart of Gold
- Chapter 7 - Holidays in the Dark
Cell Four are confronted by a naked man who can control the infected. Maeda shoots him and they leave the city for the safety of the Shouran Academy. However Hitotsukabuto Kiyoharu, the Acadamy's new leader, considers them deserters who no longer have a place there. Yamanoi proposes that if they can bring back weapons from the JSDF then they should be allowed to stay. He agrees and the boys set out again.
- Chapter 8 - Daydream Killers
- Chapter 9 - No Guy No Cry
- Chapter 10 - My Rotten Lung
- Chapter 11 - Smells Like Dead Spirit
The conclusion of the JSDF weapon retrieval story arc. Cell Four search the JSDF garrison for weapons, encounter a new breed of the infected, and meet the naked man again. Kasahara Yuuji, Hanabata Shinpei and Hanabata "Rikkun" Riku are introduced.
- Chapter 12 - He's Electric
- Chapter 13 - Picture of Rikkun
- Chapter 14 - Roll Over Wagner
- Chapter 15 - Life On Fort?
The death of the 1st Bokor story arc begins. The naked man, now known as the "Bokor", is brought to the Shouran Academy for examination. He breaks free from his restraints in an attempt to find and capture Maeda. But when the Bokor finds him, Hitotsukabuto helps Maeda avoid the Bokor's deafening sonic blast. He then shoots the Bokor in the head at point-blank range!
- Chapter 16 - The Adventures of Rain Dance With Bokor
- Chapter 17 - Nowhere Man
- Chapter 18 - Yoshiaki, Can You Hear Me?
- Chapter 19 - Long Tall Daisy
The conclusion of the death of the 1st Bokor story arc. The Bokor recovers from a near-fatal gunshot wound and tries to escape from the Academy. He is captured and killed, but infects Maeda in the process. Maeda’s arm is amputated to prevent the spread of the virus. It is then decided that the Bokor has been targeting Maeda because only Maeda can contract his strain of the virus. Soldiers appear at the Academy.
The soldiers are actually members of the "Child of Light" cult, people who worship the Bokor as God. Cell Four (without Maeda), Hitotsukabuto, Kasahara and Hanabata fight against the cultists, but are unsuccessful. All but Hitotsukabuto are captured; the rest are herded to a rooftop and sentenced to die. Kasahara and Shinpei are kicked off the roof. Refusing to let the cultists decide their fate, Yoshioka, Iwakura, and Yamanoi jump to their deaths.
- Chapter 24 - The End of The Crazy World
- Chapter 25 - Sympathy for Slaves
- Chapter 26 - Damned Damned Damned
- Chapter 27 - Survive on Wild Side
Maeda rescues his friends (All but Kasahara, who was killed by the zombie hordes before Maeda assumed control) and defeats the Child of Light cultists. Cell 4 questions him about his new found abilities. The Academy receives a mysterious phone call from Dr. Yukko Sakagami, who asks them to help her save the world.
- Chapter 28 - With or Without Oedipus
- Chapter 29 - If You Want Dirty Blood
- Chapter 30 - Everybody's Dying
- Chapter 31 - A Rush of Blood to the Melty Head
Dr. Sakagami Yukko explains that there are actually two viruses, the M-Virus and the F-Virus. She claims she can cure the M-virus with a sample of the F-virus from a newly infected human. Cell Four and Shinpei agree to deliver F-virus infected Maeda to her on the Sea Firefly. While en route Yamanoi reveals that he too is an F-virus carrier. They reach the Tokyo Bay Aqua-line, a bridge-tunnel that leads to the Sea Firefly.
- Chapter 32 - Black Rainy Sabbath
- Chapter 33 - Mitsuru Traubert's Blues
- Chapter 34 - Tender Than Bombs
- Chapter 35 - Only Shallow
Cell Four, Shinpei and Riku Hanabata enter the Tokyo Bay Aqua-line tunnel. They progress deep inside but are stopped by a car pile up, a horde of zombies and carbon monoxide poisoning. Yamanoi's mind continues to deteriorate and his reason for incarceration is revealed. He devises a plan to escape and sacrifices his life in order to carry it out. The group reach the Sea Firefly and rescue Dr. Sakagami Yukko from dog like zombies in the process.
- Chapter 36 - Wouldn't It BeScared
- Chapter 37 - Grateful When You're Infected
- Chapter 38 - Big Boys Don't Cry
- Chapter 39 - New Born
- Chapter 40 - Burning Fly (For A Pretty Baby)
- Chapter 41 - No Sadness
- Chapter 42 - Once Upon a Time in Africa
- Chapter 43 - Bitter Acid Symphonie
- Chapter 44 - Giant Anger
- Chapter 45 - Guaranteed
- Chapter 46 - The Future is in their Hands
- Extra 1-Common Lovers
- Extra 2-King biscuit game
- Extra 3-All apologies
The group betrayed by Dr. Sakagami who takes Maeda and reveals that the virus is concentrated in the Cerebro-Spinal Fluid. Hitotsukabuto stops her attempts to kill him and explains that Daisy was infected. Maeda decides to control Riku and use him to attack the other Bokor in order to get the necessary samples. This fails as a second Bokor appears and the two merge to create a giant Maeda. Iwakura knocks Maeda out and confronts the giant himself. Maeda finds out that Iwakura was crushed by the giant under a large concrete pillar, and his anger suddenly grants him the power to control the zombies. He succeds in killing the two Bokors. It is then revealed that Iwakura miraculously survived. Fast-forward by two days, and Dr. Sakagami announces the cure's completion. She gives several doses of it to the group and all but Maeda and Iwakura go their separate ways.