The seven boys have become comrades and spend time working out in their cell. Joe reveals that he has a younger sister on the outside. Seeing her again is his sole motivation to endure the school. Joe later receives a visit from the orphanage administrator where his sister is staying saying his sister is about to be adopted. Afraid he will not see her again, Sakuragi and the other boys cause a distraction allowing Joe to escape through an unguarded entrance. The boys are beaten and placed in solitary confinement. Turtle recounts losing his entire family in the atomic bombing of Hiroshima and why he helped Joe escape. Joe arrives at the orphanage and attempts to escape with his sister but is caught by the police. Joe's sister 'rejects' him and sends him away (in an attempt to protect him). Distraught, Joe is returned to the school and placed in solitary.

Joe leaves solitary and Sakuragi's words are able to comfort him. Joe resolves to survive and one day reunite with his sister. Ishihara tells Uncovered that Sakuragi murdered his parents. Uncovered confronts Sakuragi in the mess hall, resulting in the two almost coming to blows. Sakuragi is taken and beaten by Ishihara who greatly hates Sakuragi for being the lone student in the school who is not afraid of him. Uncovered remembers his early childhood being poor and how his mother was sexually exploited to get food, causing him to develop a distrust in others. Ishihara discovers Uncovered with a stash of hidden cigarettes. Using Uncovered's fear of him, Ishihara schemes to implicate Sakuragi. A fire, ignited by one of Uncovered's tossed cigarettes, causes an evacuation of the cells. Uncovered is horrified when Ishihara purposely throws away the key to Cell 6, in an attempt to kill Sakuragi. Sakuragi confronts Uncovered outside and learns the other boys are trapped in the burning building and rushes back inside in an attempt to save them.

Uncovered can't believe Sakuragi would risk his own life for someone else, believing that you can only rely on yourself. Sakuragi arrives at the cell, but can't open the door. The building begins to collapse and Sakuragi is knocked down by flaming debris. Outside, Uncovered searches for the lost cell key and locates its. Ishihara arrives and demands the key but Uncovered refuses to give it up. Uncovered enters the building and saves Sakuragi and the others. They escape and then Sakuragi knocks out the shocked Ishihara. Sakuragi is taken to the hospital to recover from his injuries. He tells a nurse about how he greatly admired his father, a soldier. However, after the war, his father returned home a broken man. One night, Sakuragi confronted his father saying he had lost all respect for him. A short time later, Sakuragi's father commits suicide. Sakuragi believes he 'murdered' his father, because he didn't try to understand his father's pain and believes his hurtful words drove his father to kill himself. Sakuragi doesn't want to lose anyone else important to him and that the other boys are his best friends. Overhearing this story, the bond between the seven becomes even stronger.

After leaving the hospital, Sakuragi reunites with his cellmates. A new guard, Kumagai, has replaced Ishihara who is on house arrest related to the fire. While doing community service outside one day, the boys each relate their dreams. Before returning to the school, the boys carve their dreams into a large tree and promise to meet back at the spot after they get out of the school. Ishihara returns and conspires to with Dr. Sasaki to deal with Sakuragi, who will be released in a month. They remove Sakuragi from cell 2-6 and place him in another cell with several large, strong boys. They beat him nightly, yet Sakuragi continues to bear the pain and smile, frustrating them. Mario, learning of the beatings, begs to take Sakuragi place in exchange for them sparing him. They beat Mario and shatter his right hand with a large stone. That night, the bullies taunt Sakuragi with what they did to Mario. After hearing they shattered Mario's hand, Sakuragi pulverizes the ringleader's face with a single punch. The other bullies stare in shock as Sakuragi's tells them that he was willing to put up with their abuse, but that they crossed the line when they attacked his friend.

The other bullies attack Sakuragi, while Ishihara listens from outside the cell. Ishihara leaves content that Sakuragi will be bludgeoned to death by morning. In the morning, Ishihara opens the cell, but is horrified to see all the bullies beaten and bloody on the floor. Cowed by the beating they suffered, none of the bullies are willing to admit it was Sakuragi's fault, causing Ishihara to leave in a rage. Unable to intimidate Sakuragi, Dr. Sasaki suggests Ishihara make Sakuragi break the rules by hurting his friends. Realizing Ishihara's goal, the boys bear the abuse to protect Sakuragi. Sakuragi, no longer able to watch, grabs Ishihara and is in turn placed in solitary confinement. Ishihara plans to starve Sakuragi to death saying that he and Sasaki can't let him out because of what he knows. One year earlier, Sakuragi had a roommate named Ei'ichi who was sexually molested by Dr. Sasaki. Unable to live with the constant abuse, Ei'ichi committed suicide. Guard Kumagai reveals Ishihara's plans to the boys in 2-6. Turtle manages to sneak food to Sakuragi's cell, restoring his will to survive.

Ishihara is apoplectic that Sakuragi is still alive after more than two weeks of starvation, unaware that Turtle and later Guard Kumagai have been sneaking him food. Kumagai tells Mario and Nurse Setsuko about Dr. Sasaki's involvement with Sakuragi mistreatment, unaware that Sasaki is secretly listening. That night when Kumagai brings Sakuragi food he discovers that Sakuragi is being subjected to water torture. Attempting to help Sakuragi, Kumagai is ambushed by Ishihara. Some time later after Kumagai fails to return to the hospital, Mario attempts to leave but is confronted by Ishihara, who reveals that Kumagai died in an 'accident'. Mario returns to the school and tells the others about Sasaki and Kumagai. Knowing Sasaki and Ishihara will not allow Sakuragi to leave alive, Mario and the others plot to free Sakuragi and escape, despite knowing that they'll be sent to juvenile prison if caught.

Uncovered devises a plan to free Sakuragi and shares it with the others. Needing to get a key from Dr. Sasaki, Joe volunteers to go to the doctor's office, despite knowing Sasaki's perverted lusts. Joe fakes a stomach ache and is taken to Sasaki's office, where he 'flirts' with Sasaki. Joe convinces Sasaki to strip naked, and when his back is turned Joe strangles him with a cloth rope and ties him up. He returns to the cell and releases the other boys. Reaching Sakuragi's cell, Mario knock Ishihara unconscious and they carry Sakuragi away. A guard finds Dr. Sasaki tied up and sounds the alarm. Uncovered 'sacrifices' himself to draw the guards attention and manages to cut the electricity to the compound and search lights. At the front gate, Cabbage and Soldier stay behind to block the guards. Outside the compound, Ishihara ambushes the others and tries to stab Sakuragi with a knife, but Mario pummels Ishihara unconscious again. After eluding capture, Mario becomes depressed about losing the others, but Joe and Turtle state that it was Mario's determination which allowed them to save Sakuragi's life.

After hearing about the escape, Nurse Setsuko encounters Turtle and gives him directions to an unused farmhouse, where they can hide and treat Sakuragi. Setsuko brings medicine, food and clothing, committed to keeping a promise she made to Mario. At the school, Uncovered, Soldier, and Cabbage are put in solitary and Ishihara subjects them to the same water torture he used on Sakuragi. Sakuragi regains consciousness and asks them to return to the school. Later, Dr. Sasaki and Ishihara are shocked when Joe returns, and they attempt to intimidate him. They're confidence quickly turns to horror when Joe reveals that he knows about their involvement in Ei'ichi's suicide. He also reveals that Sakuragi has Ei'ichi's suicide note, which could send Sasaki and Ishihara to prison. Using this information as leverage, Joe gets Cabbage, Soldier, and Uncovered released from solitary and they are no longer beaten or abused. Sakuragi continues to heal while Mario practices boxing. In the market one day, Mario and Turtle meet a woman who is promoting boxing matches at a nearby American army base. Mario enters a boxing match with an American boxer and is completely overwhelmed by the man's size and power. After the match, the promoter woman, Lilly, gives Turtle and Mario money and tells Mario to get stronger. Shamed, Mario resolves to pay Lilly back ten times over.

Sakuragi begins training Mario in boxing so he can win his next match. Turtle takes a job selling black market goods. At the school, Soldier learns that he's been accepted in the Japanese Defense Force and will be leaving the reformatory early. At the farmhouse, Setsuko suggests she and boys take a photo and later borrows a camera from a coworker at the hospital. Dr. Sasaki overhears her conversation and sends Ishihara to follow her, discovering Sakuragi's location. When they're alone, Setsuko confesses her feelings to Sakuragi. Sakuragi and Turtle accompany Mario to his next match, unaware Ishihara is following them. Turtle goes to the nearby market before the match, but is caught by the police. Learning Ishihara was responsible, Turtle attempts to phone the others. Lilly tells Sakuragi and Mario about Turtle being caught and Sakuragi leaves to find a phone. Mario begins his match determined to win. Elsewhere, Dr. Sasaki plots to dispose of both Sakuragi and Ishihara, who is now using speed and has become a liability.