Seitarou Tanabata is all fired up for his first teaching job at a high school But Nanba Building 13 High School l is filled with delinquents. The students are troublemakers and even the teachers are odd. Seitarou is already bullied by 4 students in the 3rd year, class 13 on his first day. Then, the number 1 troublemaker, Hajime Sugoroku, returns after serving his suspencion. Can Seitarou ever become the teacher he always wanted to be?
This is “Nanba Prison,” the large impregnable prison somewhere in the territorial waters of Japan. On this night, 4 inmates recklessly attempt to escape from the world’s best prison guards and security. Jyugo, who wears mysterious shackles. Uno, a self-proclaimed ladies’ man. Niko, an otaku who’s prone to illness. Rock, a foodie gang member. Can the inmates of Building 13, Cell 13 pass security and reach outside of prison in one piece?
The inmates in Cell 13; Jyugo, Uno, Niko, and Rock are spending their days escaping, creating mischief, gossiping, and sometimes, working. These troublemakers are giving a headache to supervisor of Bldg. 13, Hajime Sugoroku. Warden Hyakushiki has ordered Hajime to submit files regarding the 4 inmates. Hajime is then ordered to give a report about the 4 who are known as repeat offenders of jail-breaking. Afraid of losing his job due to the cover-up, Hajime does his best to create the new files...
Jyugo and the gang are killing time teasing the new guard, Seitarou. One day, a new inmate is sent to Cell 13. Inmate Number 99, Tsukumo. He looks and acts like a ninja! Uno, Niko, and Rock are excited to see the real thing. But as a Japanese, Jyugo does not believe him. To convince Jyugo that he’s a true ninja, Tsukumo challenges Jyugo to see who can escape from prison.
Nanba's New Year Joint Cooperation Tournament, aka New Year’s Tournament, begins by gathering the entire inmates. Jyugo and the others are enthused once they hear the winner gets to choose whatever he wants. However, all the matches are odd events relating to New Year’s. Can Building 13 win against the other inmates led by peculiar guards?
Jyugo and the gang are advancing through the New Year’s Tournament without a hitch. In the Hyakunin Isshu event, Uno wins against the Building 3 inmates, Trois and Honey. The 4th event is a physical match revolved around a spinning top, but Niko unintentionally enters the match. The opponent is Upa, a kung-fu expert from Building 5. Does Niko, the otaku, have any chance of winning?!
Cell 13 has advanced their way to the final event of the New Year’s Tournament. Jyugo and Hajime are battling against the Building 4 supervisor, Kenshirou Yozakura, and an inmate named Musashi. Jyugo is surprised to see Musashi again. Musashi, in search for the “man with the scar on his neck,” attacks Jyugo mercilessly. Soon as Jyugo hears about the man with the scar on his neck, something odd starts happening to his body.
Tsukumo heads to the visiting room during the break from the New Year’s Tournament. His manager, Hattori, has come to visit. People think the famous action star is missing and has no idea he’s in prison. Hattori persuades the talented Tsukumo to come back into stardom. However, already uninterested in being a star, Tsukumo talks about his upbringing.
The shackles have been triggered and Jyugo’s hands transformed into blades. He attacks Musashi and splits the arena in half. The arena becomes chaotic and Momoko orders Hajime, Kenshirou, Samon, and Kiji to apprehend Musashi and Jyugo. Musashi retaliates against the guards while Hajime stands in Jyugo’s way.
After causing a catastrophe in the New Year’s Tournament, Jyugo and Musashi are sent to the underground cell. To solve the mysteries of their powers, Kenshirou suggests allowing the two to speak to one another. Unable to move freely, Musashi gives Jyugo information on the man with the scar.Listening to their exchange, Hajime tells Jyugo he’s empty. Hajime’s words confuses Jyugo.
Hajime has been given a three-day suspension due to beating Jyugo at the New Year’s Tournament. Momoko orders Kenshirou, Kiji, and Samon to take turns covering for Hajime. But Uno, Nico, and Rock do whatever they want as usual. The three supervisors constantly struggle to maintain order with the three troublemakers. Finally, after three days, Jyugo is back...
Building 13 Cell 13 has won the New Year’s Tournament. Rock receives a stone oven and Nico receives the latest video game everyone can play with. Rock and Nico invites inmates from other cells to show their prizes. The two are very satisfied and they both thank Jyugo for that.
Musashi discusses more of his past prior to meeting the Scarred Guard with Kenshirou Yozakura. Uno gets everyone from the New Year's Tournament together to play in the game room he got for Cell 13's victory in the tournament. Later, Jyugo leaves Cell 13 for some fresh air at night, only to encounter Elf.
Jyugo meets Elf, who threatens to use those close to him as experiments, just like him and Musashi. Following the next night, Cell 13 breaks out of their cell for fun, but Jyugo intends to really escape so Elf will chase after him and leave the others be. Hajime, however, is determined not to allow Jyugo's passage.
Jyugo escapes from prison again and Hajime Sugoroku goes looking for him, but it’s a usual day for the inmates and guards. Many things have happened, but it seems like nothing has changed in Nanba Prison.
A new guard has come to Building 13, and not everyone is happy about it.
Yamato takes Rock and Tsukumo to Building 5 for training. Rock challenges Samon to a duel, but he is defeated by only one finger.
Rock and Yamato suddenly become violent after returning from Building 5 and attack Jyugo and Seitarou. Covered in bruises, Jyugo tries his best to protect Uno and Nico.
Hajime, Jyugo, Uno, and Nico head to Building 5 to find out about Rock and Yamato. Jyugo and the others fall into a trap and end up in the level 1 underground cell. There, they find the captured Upa and Liang.
Jyugo, Uno, Nico, Liang, Upa, Honey, and Trois make their way through Building 5's underground cell to find the captured guards. They hide in the file room where Jyugo finds some shocking information about himself!
The escaped convict, Hachiman, appears in front of Liang and Upa. Meanwhile, Uno and Jyugo are concerned about Nico, who doesn’t have his medication. It seems something horrible will happen to him if he doesn’t take his medicine.
Uno explains to Honey and Trois that when Nico's medicine wears off he goes out of control. As Nico's alternate persona awakens, he fights Hachiman. In the meantime, Liang and Upa restrain Daisen Rokuriki and destroy his talisman. Qi interrupts the fight and while Nico attacks him, he injects Nico with his medicine, rendering him unconscious. Hachiman feels as though he has won, however, to his, Liang, and Upa's surprise, Qi injects poison into Hachiman's leg. While Hachiman is unconscious, Upa, Liang, and Qi talk. Hachiman eventually regains consciousness, and tries to fight the trio, but he's taken down by a group attack.
Upa wonders if someone other than Enki is involved in the situation. Meanwhile, Jyugo and his group reach level 2 where they are confronted with numerous Jiang-Shi dolls. As Trois explores the area, they encounter Ruka Gojou and other guards with talisman on their foreheads, Daisen Kokoriki and Daisen Youriki. Trois tries to defeat him with a handmade a flame-thrower he made with leftover parts. Just as they think they are free, Ruka Gojou appears and captures Jyugo.
Jyugo has been captured by Ruka Gojou, but is saved by surprise attack from Trois. Honey gets frustrated with Jyugo's uselessness and wants to leave him behind. Eventually, Ruka, Daisen Youriki and Daisen Kokoriki catch up to the group and Jyugo is caught by Youriki. While trying to help Jyugo, Uno is restrained by Ruka. Though initially reluctant, Honey decides to help. The two inmates of Building 3 decide to repay their debts to Jyugo and Uno, and deal with Ruka and the Daisens. After managing to subdue them, Ruka surprisingly comes out unscathed, now prepared to fight them seriously.
As Ruka begins to fight seriously, Trois and Honey pursuade Uno and Jyugo to go ahead while they continue fighting but Jyugo eventually returns and defeats Ruka with his blades. Kokoriki and Youriki later arrive and try to arrest the escaped inmates. As they escape, Uno, Honey and Trois come up with a plan while Jyugo begins to make his way to Hajime.
Enki realises the prisoners have escaped as Mitsuru and Kenshirou begin questioning the situation. Meanwhile, Trois and Honey free Kiji who takes care of Daisen Kokoriki and Daisen Youriki before defeating Ruka. Jyugo finally finds Hajime before freeing him and Samon from their cells. Kiji handcuffs the inmates, but they are suddenly confronted by a hoard of surveillance dolls as are Jyugo and Hajime.