The story concerns the people of a small Japanese town by the name of Kurôzu-cho, and how they become obsessed by the occurrences of natural and artificial spirals around them. The result of this obsession is a slow transformation into something other than human, leading to a gruesome, realistically-depicted death.
This manga is all done in pen and ink.
- The Spiral Obsession Part 1 - High school student Kirie Goshima finds out that her boyfriend Shuichi is worried about his father, who has begun a strange obsession about spirals. He collects anything featuring a spiral pattern, and eventually he stops going to work to stay at home and stare at his spiral collection. His obsession becomes so disturbing that he starts to use his own body to create spirals. Eventually, he becomes a spiral himself by contorting his body in a wash tub in the shape of a spiral, killing himself in the process.
- The Spiral Obsession Part 2 - After he dies in a strange suicide, Shuichi's father's body is cremated, but during the funeral, the smoke from the cremation forms a spiral shape in the sky, consequently driving Shuichi's mother to insanity. She develops a phobia of spirals and starts to rid herself of everything in her body that looks like a spiral. Eventually, she tries to rid herself of her inner ear (cochlea) with a pair of scissors. Subsequently, her sense of balance is destroyed along with her hearing and she is in a constant state of vertigo until she dies. During her cremation, the smoke creates another spiral.
- The Scar - Kirie's class friend Azami asks Kirie if she can meet Shuichi. Although hesitant, Kirie agrees, but when they go to Shuichi's house he feels a sinister presence coming from Azami's forehead, and Azami reveals that she has a crescent-moon shaped scar which she believes has the power to make any boy fall in love with her. However, Shuichi suspects that the scar is causing terrible effects in Azami, and is proven right. The scar becomes a hollow spiral that sucks what gets too close to it in, eventually eradicating Azami herself..
- The Firing Effect - Kirie's father, a potter is at the kiln late at night working on pottery. The results turn out to be horridly disfigured ceramics with spiral shapes on them. When asked if he needed help or what he was doing, he aggressively ignores the subject and forbids anyone to look in the kiln. Kirie sneaks into the cottage where the kiln is, looks inside, and sees a mass of spiral souls twisting around in the kiln, screaming of the heat. Later, when Kirie's father is questioned about where he got the clay, he says that the clay came from the bottom of Dragonfly Pond, which had been absorbing the ashes of cremated people. Shuichi tries to stop Kirie's father from creating these abominations, and the cottage burns down as a result.
- Twisted Souls - Kirie meets a former classmate who has recently been having a problem with his girlfriend's family. It seems that both families of the couple live in the same row house and are in a constant aggressive feud, and do not agree to let their kids date. Kirie decides to help her friend and his girl to escape from their parents, but the families figure it out, and almost catch them. However, the two are "contaminated by the spiral", and twist themselves into a grotesque shape similar to that of two snakes intertwined. They then swim away into the sea.
- Medusa - Kirie's hair begins to grow unusually, and when Kirie goes to cut it, the hair animates and refuses to be cut. It starts to control Kirie, forcing her to seek the attention of everybody in the town, which it has the ability to mesmerize. The problem worsens when Kirie's classmate, Sekino, becomes jealous and decides that her hair should have the same gift. A showdown for attention ends in Kirie's hair causing her to collapse, only to have Shuichi come to the rescue and cut it. On the other hand, Sekino's hair causes her untimely end, since it drained out her life force thus killing her. If Kirie's hair had not been cut by Shuichi, she would've met the same fate.
- Jack-in-the-Box - Kirie is being stalked by a seventh-grade boy named Mitsuru, who likes to jump out and surprise people, which gained him the nickname Jack-in-the-Box. When Kirie refuses to be his girlfriend, Mitsuru decides to prove his love by trying to stop a speeding car with his love for her. However, Mitsuru is killed, with his body twisted around the front wheel of the car, and he is buried (bodies are no longer cremated after previous events). Kirie still has no peace, as she receives a strange message that Mitsuru will come back from his grave. Kirie and Shuichi dig up Mitsuru's grave, only to have the corpse bound after them, the legs and abdomen falling off to reveal a gigantic spring on which he bounces along. They manage to stop him and reveal that the spring was actually from the car's suspension that had become lodged in Mitsuru's body.
- Snail People - Katayama, a slow-moving, slow-talking classmate of Kirie's starts to behave strangely, as he begins only attending school when it rains. After a bully strips him naked and tosses him out of the locker room, Kirie discovers a spiral-shaped birthmark on his back. Soon the spiral shape scar begins to morph into a full-blown snail shell as Katayama turns into a giant human-sized snail. Imprisoned in a cage at school, soon Katayama's nemesis turns into a snail too and ultimately mates with Katayama. After the Snails escape from their cell together, Kirie and her science teacher find their eggs, which the teacher quickly destroys after declaring the two students abominations. However, the teacher himself comes into class several days later, having become a snail himself.
- Dark Lighthouse - The abandoned lighthouse of Kurôzu-cho begins to switch on by itself at dusk mysteriously, creating a spiral vortex of light. Anyone who is caught by its light is blinded temporarily and caused to walk in circles. Some people of the town decide to go there to investigate, but they don't come back. Kirie's brother, Mitsuo, and his friends investigate(despite Kirie's warnings). There, they discover that the main light has transformed into a freakish spiral construct which produces extremely intense heat, which killed the men sent to investigate. As dusk approaches, Kirie, Mitsuo and the friends run away, but one of them trips and is killed by the heat.
- Mosquitoes - Part one of a two-part story. Kirie is admitted to the hospital due to the burnings made by the lighthouse's light and discovers a body drained of blood on hospital grounds. Later, Kirie's pregnant cousin, Keiko, moves into her room in the hospital after suffering an attack from a swarm of mosquitoes. At first everything seems normal, but dead bodies start showing up, completely drained of blood. One night, Kirie discovers that her cousin, as well other pregnant women bit by the insects, have developed a taste for human blood due to the bites they received from (female) mosquitoes. She realizes, due to help from Shuichi, that this is related to the female mosquito's need to suck blood to give birth to their young.
- Umbilical Cord - The second part of the two-part story that started in "Mosquitoes". The pregnant women finally give birth to seemingly normal babies. To Kirie's relief, they all look normal. however, she soon realizes they all have strangely inflated bellies. After walking by the nursery, she discovers that they can talk, and plan on bartering their constantly regrowing umbilical cords and placenta (which are highly addictive when eaten, and have been given as "mushrooms" to the hospital staff) to their doctor to make him sew them back up inside their mother's womb. The Doctor succeeds at replacing the first baby, which happens to be Keiko's. Keiko becomes a ravening monster, with a long, spiral tongue that it uses to suck out blood. Kirie escapes as Keiko drinks the doctor's blood, and escapes the hospital. What eventually happens is not known.
- The Storm - When a typhoon passes by Kurôzu-cho, Kirie is caught by the typhoon's eye; somehow, the typhoon falls in love with her and begins to stalk her everywhere, causing horrible damage. After attempting to grab a woman which it mistakes for her, Shuichi then appears to protect Kirie. They shelter under a bridge so the typhoon can't see them, but its wind smashes a traffic mirror that allows it to see Kirie. After attempting to escape into a storm drain, they discover it controls the rain that falls into it, and the eye sucks them into the sky. Several days later, the Typhoon is pulled into Dragonfly Pond, and Kirie and Shuichi are taken out.
Volume 3 contains the final 6 chapters, plus an extra chapter that forms an epilogue with a story connecting to Volume 1.
- The House - After the typhoon destroyed much of the city, town officials move Kirie and her family into an apartment inside a previously abandoned row house provided. Her neighbors are a peeping tom named Wakabayashi, a mysterious couple of an old woman, who wears a hooded robe to cover up her body, and her sick son. As the woman's son dies, Kirie and her family began to contract spiral-shaped warts all over their bodies, and the sores quickly turn into spikes. Realizing that the house is causing their body-disfiguring disease, another hurricane hits the town just as Wakabayashi becomes a horribly disfigured monster with spikes all over his body, even coming out of his eye sockets. As the family flees the house, Wakabayashi is killed by a piece of debris which impales him. The narration box explains that once they left the house, their spike sores vanished.
- Butterfly - Maruyama Chie, an anchor woman, comes to the town with her co-workers in a van, only to be chased by a typhoon. Only Chie survives the car crash, and she travels into the town, seeing ruins and dead bodies everywhere. It is revealed that twisters form with nothing more than a sudden movement or a loud noise, which makes the (still-functioning)time sirens a large problem. It appears that the previously abandoned row house apartments around the town is the only sort of shelters not destroyed by twisters, so every apartment becomes crowded and tension amongst dwellers tightens. Chie befriends Kirie, who makes the strange discovery that the snail people have returned. Later, everyone living in the row house discovers that the boys that have been terrorizing the village have learned to ride the twisters like butterflies.
- Chaos - The gangsters and some young men form a gang called 'Dragonfly'. They destroy buildings for fun and rob food from rescue teams. Snail people begin to appear again after long being unseen. The apartments become more and more crowded and people begin to quarrel with one another without proper causes. By helping Shuichi from a conflict with another man, Kirie's family is cast out from the apartment. As they wander to find a new place to shelter, they witness the Dragonfly gang cooking snail people as a meal. They say the meat is delicious, and try to force Kirie and Chie to join their gang. Kirie refuses and the Dragonfly gang unleash their hurricane power against her and her friends. It is this power, however, that kills them when they are sucked into Dragonfly Pond.
- Erosion - It soon becomes apparent that the horrific force behind the nightmare destroying the town are now keeping the townspeople from escaping, as the main tunnel leading out of town becomes a never-ending spiral, while giant whirlpools sink all ships that try to evacuate the town. The row houses become overly occupied until they crash into pieces of wood, revealing that the townspeople have become strange creatures with spiral-shaped bodies. Though rescue workers still enter the city, the food being brought runs out and many would-be rescuers soon find themselves becoming snail people. Forced to eat snail people's meat left over by the Dragonfly gang and missing her father, Kirie soon finds out that her younger brother Mitsuo is in the process of turning into a snail. Desperate to save her brother from his fate, Kirie vows to leave the town.
- Escape - Kirie and her friends flee the town, in hopes that once they leave the area, that the spiral curse turning her brother into a snail will be reversed. As they flee, they the come across a once-rescue team that they had met earlier, now obsessed with eating snail meat, ultimately targeting Mitsuo when they find out he is becoming a snail. Mitsuo finally transforms and Kirie forces him to flee down a cliff's side to escape the group, who all become spiral creatures when the leader begins talking about how he wants to crawl into Mitsuo's shell and eat his flesh raw, like he did to another snail earlier.
- Labyrinth - Kirie's group finally comes out of the woods, only to discover that they have returned to the town. They also discover that several years have passed while they were away, and the remaining townspeople have repaired and expanded all the old row houses, revealing that they connect together form a giant spiral-shaped labyrinth with the lake at its center. Shuichi theorizes that the strange events have happened again and again through the ages, always ending with the rebuilding of the spiral apartments. After all is over, the apartments are slowly ruined and all traces vanish, and a new town is built. The reason why no one knows of this is because all the people have vanished after the events, and the only memories that one could have are removed. Kirie, Shuichi and Chie follow the labyrinth to its center, but Chie is trapped within one of the quickly finishing row houses, and Kirie and Shuichi must continue without her. When they reach the center, they discover that Dragonfly Pond has dried up and been replaced by a long spiral-shaped stairwell that goes deep into the earth.
- Completion - Without any other choice, Kirie and Shuichi follow the stairs into Dragonfly Pond and discover a huge cave with a lot of gigantic, spiral-shaped towers and buildings, with a huge, glowing spiral-shaped stone in the center. They find all the corpses of the spiral-shaped inhabitants of the towns, who have begun to turn to stone, Kirie's parents included. All the corpses have a pleased look to them, and are all staring at the spiral stone. It appears they have become part of the city and the spiral itself. Shuichi is wounded after an earlier attack, and is unable to leave the cave, asking Kirie to leave him. Kirie refuses and decides to stay with him. As they hug each other, their arms become spirals that bind them together. The stairwell begins to close, thus imprisoning Kirie and Shuichi and ending the spiral curse for now, perhaps to return later, when a new town is built around the lake.
- Lost chapter: Galaxies - Strange-looking radio galaxies are discovered in the night sky, which begin to have strange effects on the residents of the town. People begin to have the ability to send and receive "radio waves", which leads to several murders. As the story ends, a psycho attempting to kill Kirie is converted into a miniature galaxy himself, and escapes into the sky. At the end, it is revealed the galaxies were only visible within the town, and thus all the arguing was for naught. Judging by the length of Kirie's hair, this story takes place some time before Medusa.