The story revolves around "Minimum" or "minor miracle"— special hereditary powers discovered only in an extremely limited number of humans. Those who possess such powers are known as "Minimum Holders." Partners Nice and Murasaki form a detective agency called "Hamatora" in Yokohama in 2014 — but their "office" is a table at Cafe Nowhere where they and their friends wait for clients. An old acquaintance of theirs, a cop named Art, hires them for a serial murder case he is investigating, and they discover that the murder victims are all "Minimum Holders." As Minimum Holders themselves, Nice and Murasaki are drawn into this case, whether they like it or not.
Hajime's power takes down one Minimum Holder before falling asleep. Society becomes desiring of obtaining their own Minimum afraid of the attacks from Black Cosmos. However, Birthday, Ratio, Honey and Three work together to take down Moral's allies. As Momoka sees every fight scene, she is found by Gasquet. Murasaki handles Moral's last underlings while Nice confronts Moral personally in a ship. There, Moral reveals he unleashed the Forbidden Minimum Holder on himself which allows him to overwhelm Nice. Moral then explains how he has captured the Minimum Holder Hibiki whose ability will be used to torment non-Minimum Holders. As Moral keeps beating Nice, Murasaki tries to aid his partner but suffers a similar fate. Theo and all of the people that were aided by Nice try to bring him support but he is annoyed by their repeated messages. Nice keeps fighting and manages to overwhelm Moral whose body deteriorates as a result of having two Minimums. He is then approached by the seemingly alive Art who kills Moral and points his gun at Nice.
Itou Shouko of the Association for Health, Protection and Equality of Youths contracts Hamatora to search for a scandal within Facultas Academy. Meanwhile, Art questions Professor Moral after learning that the Association had been providing large quantities of the Nemcrois drug for his research into non-innate Minimum Holders. Moral explains his warped interest into a world where everyone possesses Minimum abilities and taunts Art on his graduation from Facultas despite not possessing a Minimum. Meanwhile, a large monstrous figure crashes a public Association meeting and reveals itself as Itou's son, Takahiro before escaping. As Art makes his way to the scene, Moral implies that he had given the Minimum ability to Takahiro, with the former swearing to arrest him. Afterwards, Nice blames Itou for Takahiro's change. Realizing that he was being challenged however, Nice approaches Takahiro while Moral also comes to the same conclusion as Takahiro, that it would be worth challenging Facultas' top graduate—Nice to see if he had surpassed natural Minimum Holders with his abilities. However in the end, Nice makes quick work of Takahiro. In the epilogue, Moral burns down his facility and escapes before Gasquet can arrest him. At the same time, Itou's assistant severs his support of Moral's research. Unperturbed, Moral then sets his sights on Nice.
Ratio and Birthday work on a case involving a kidnapped artist. As the two interrogate a friend from the victim, Birthday is kindapped by another person and Ratio remembers his and Birthday's past.
Nice becomes involved in the case to arrest Moral and his constant recommendations offend Art. Gasquet notices the recent changes in Art's behavior and asks Honey about his past. Honey explains Art went to the Facultas Academy with his late younger brother and as a result of not awakening his Minimum he has been forcing himself to stand out despite not having it. Art's teacher, Three, takes the young man to train together and remind him that despite not having a Minimum he has already proven himself. Meanwhile, Nice and Murasaki receive a job from an man whose abuse on women result in a group of people trying to beat him up in revenge. Having to calm both forces using force bothers Nice and decides to go meet Art. Art finds Moral in the near his brother's grave and the criminal reveals his intentions to make everybody Minimum Holders so that they become equals to Nice, whom he admires. Following Art's refusal to receive a Minimum, Moral stabs him and kills him as Art tries to answer Nice's phone call but not before revealing him an unknown truth.
Momoka invites Hajime to her limousine under the promise she knows about her forgotten past. Nice becomes nervous when deducing Hajime left with is Momoka and decides to search for her. Momoka explains to Hajime that she has a power that nullyfies Minimums which resulted in Murasaki being her first victim and the rest suffering from sideffect. Momoka guides Hajime to a basement where she is attacked by berserker people whose musculature was increased. Hajime recognizes them as test experiments performed by Facultas. Hajime was the only one who was not affected by the experiments and remained locked in a cell until a young Nice met her. Upon realizing Hajime's state, Nice invited her to the outside world. After the flashback, Koneko leaks Hajime's location to Nice who goes to search for her alongside his friends. Hajime then remembers how during her escape from Facultas Nice was shot which causes her to unleash her berserker Minimum. Art identifies it as the Nihilist Minimum capable of eradicating other Minimums just as Nice comes to retrieve her.
n Nowhere Café Nice and his friends remember how three months ago Art tried killing Nice, shooting him twice in the body but Murasaki escaped with him. Ratio and Birthday go in the search of their friend Chiyu who disappeared three months ago. They eventually find a club named Freemium full of Minimum Holders and Chiyu has been hiding there. Elsewhere, Nice and Murasaki contact officer Gasquet and learn Hikaru has been wounded and is resting in the hospital. Art then goes to the Minimum Holder academy Facultas, entering by force. Nice and his friends chase after Art who attacks a group of students, calling their abilities a sin. Art is confronted by Facultas' tutor Paper who uses his Minimum to deal mortal wounds on him. As Art appears to be killed, his own Minimum is activated and restores his health. He then uses Hikaru's Minimum to trick Paper and steal his own Minimum. Art then leaves the area much to Nice's confusion.
Nice and Murasaki infiltrate Yokohamabane High School following a request from two students named Theo and Rei to search for their missing teacher, Yasuo Kitazawa. Sometime later, Art summons Nice and Murasaki after discovering the murdered Kitazawa in a burger restaurant and explains the serial murder case to them. Nice also steals Kitazawa's phone from the crime scene and obtains the six photos of Theo's bullies supposedly leaked on the internet. Nice then traces the poster's IP back to Kitazawa's home and deduces that he had been using his Realism Minimum to turn descriptions of the bullies' exploits into pictures which he then used to further his reputation over their exposure. Afterwards, as the Hamatora PI's establish a link between the photos and the recent serial bombings, Theo stumbles upon his former bully and the serial bomber, Kojima in his latest bombing attempt at the school using his Time Acceleration Minimum. However Nice and Murasaki show up just in time to foil the bombing. Afterwards, Art discovers that Kojima and the Gravity Holder obtained their abilities artificially which would require the use of a Minimum Holder's brain. Elsewhere, the serial killer admires his collection of brains.
While Hamatora helps film a commercial as a publicity stunt to cover up Takahiro's rampage, Art has Minimum Holders—Honey and Three assist in a case. This causes Honey to misplace her briefcase for one filled with totem poles at the airport. Elsewhere, Art and Gasquet follow up on a string of attempted robberies committed by minors using guns obtained via a threatening email which also predicts an insurrection. While a group of men kidnap Honey because of the briefcase, Art enlists Nice to help in the gun case. Three eventually rescues Honey and discovers the kidnappers to be smuggling gun parts into the city. Afterwards, Nice establishes a link between the gun case and a popular online video by Katsuragi Yuuki using subliminal messaging while unaware that Moral had been the one manipulating Katsuragi. Meanwhile, Honey tracks down her briefcase from a smugger and discovers that the totem poles contain gun parts. After relaying this to Art, he has her predict the location of the insurrection and the police foil it just in time with Hamatora's help. Afterwards, Art and Nice discover the murdered Katsuragi at his home and Nice likens to himself to the mastermind despite having no knowledge of Moral's connection.
After Gasquet's funeral Nice and his friends start investigating who attacked the prison of Minimum Holders and find his killer. Nice and Murasaki meet local information broker Mao who informs them how Gasquet contacted him to request him information about Saikyo. Although the culprits managed remove evidence of them, the group manage to find a video involving the members from Freenum. They try going to the club to confront them but learn they have already left. As Nice leaves Murasaki, Murasaki has an internal conflict as he admits detesting his own weakness for being always with Nice. He is then approached by Art and Murasaki claims he wants to join him. In Art's hideout, Art realizes Murasaki is just using him to aid Nice and allows Murasaki to beat him up while Freenum records and leak the scene. When Murasaki shoots Art, Freenum's Ishigami Shunichi activates Art's Regeneration Minimum revealing him to the public as a messiah-like figure. Hours later, Nice and Hajime find a bag with Murasaki inside.
In his hideout, Art kills himself so that his Minimum would generate his body alongside his life. Meanwhile, Honey is told by her comrades how she lost her senses in the previous night when using her Minimum. Not believing it, she uses her powers, causing her to act like a child again as an apparent sideeffect. Honey later receives a bodyguard request from her father, Doktor, a consultant to the Minimum Agency's medical department who has been pursuing stray Holders. Doktor later cancels the job and an angered Honey remembers how her father aimed to use her powers for assassination jobs. Concerned with Doktor's plans regarding Holders, the people from Freemium kidnap him alongside his daughter. Three receives an alert from his partner and goes to find her with Nice, Murasaki and Hajime. Eventually, Honey uses her Minimum to send Three her future location at the cost of regressing again. Three activates his own powers and saves both Honey and Doktor before their car is destroyed. Meanwhile, BIrthday and Ratio finish his respective jobs but both experiences sideeffects regarding his Minimum (Birthday start licking batteries and Ratio is weakened). Finally, Nice, Murasaki and Hajime are given the culprit's location but they are intercepted by Art.
Nice and Moral go to the Nowhere Café as the disturbance in the streets increases. Nice explains that thanks to Honey he was able to find Moral and asks him what he did to Art. After explaining to Nice he already knows the answer, Moral talks about how the Essence is a substance he extracted from an innate Minimum Holder's brains to unlock new powers. Using Essence, Moral wishes to create a world with equality and Nice agrees with some of his ideals. Meanwhile, Ratio has Chiyu treated while Honey and Three are requested help with the riots by the police. Moral then explains his motivation to "save" Nice by making others equal to him but it makes Nice laugh for his decisions of who is weak and strong. Murasaki then fights Minimum Holders causing disturbance alongside. The civic center against Minimum Holders is then attacked by a tank. Moral leaves Nowhere by threatening Koneko, promising Nice he will fight him after finishing something. Takahiro and Hajime go to the civic center to protect the former's mother from the Minimum Holders. He then starts mutating again to fight his enemies. Takahiro is victorious and his mother thanks him. Staring at the situation, a saddened Moral makes Takahiro's body explode angering Nice while Hajime unleashes an unknown power.
In the Minimum Agency, Doktor becomes concerned with Freemum's actions and states his desire to control Minimum Holders. Meanwhile, all the subjects held in the basement where Hajime was located are being transferred to a hospital. Honey and Three then go to Nowhere Cafe to hire Nice and the rest as actors for The Tale of the Bamboo Cutter to help Three's orphans. Hajime is given the role of Princess Kaguya while the rest aim to take the other leading role. Ratio, Birthday, Murasaki fail the role while Nice only makes her smile. Meanwhile, the members from Freemum aim to make Art an idol for Minimum Holders and make Yokohama their own territory. At the same time, Doktor aims to murder all Minimum Holder causing riot. Later, Three gets the role of taking Kaguya away by default for the play. However, this reminds Nice of Hajime's past in Facultas causing him to improvise and take her hand much to everybody's joy. Later, as Birthday and Ratio reflect on Nice's change of attitude, the former starts suffering symptoms from his illness that once almost killed him. In the epilogue Nice finds a letter from Hajime directed at him.
The people from the detective agency based in the Nowhere Café in Yokohama mourn the death of their comrade Nice said to have perished during riots three months ago. When a client arrives to request a job involving a stalker, Hajime decides to replace Nice and forms the Hamatora Mark II alongside Murasaki. Meanwhile, the rest of the Yokohama group, Birthday, Ratio, Honey and Three are having less jobs than usual due to the riots involving Minimum Holders. Hajime and Murasaki's job is interrupted by Hikaru, a Minimum Holder who soon becomes a celebrity. When the Hamatora Mark II receives a murder request from a client, they instead become bodyguards of Hikaru through his producer. Hajime and Murasaki learn that Hikaru has attracted several girls but is unwilling to accept or reject them. One night, Hikaru allows himself to be the victim of the girl who wants him dead but she is stopped by Murasaki. The girl brings a group of thugs jealous of Hikaru and Hajime and Murasaki start fighting them. They are aided by Nice who is revealed to have been alive and has learned that the producer wanted Hikaru dead. After defeating the enemies, Nice is welcomed back in Nowhere Café by his friends who stop pretending he is dead. Murasaki then asks Nice why did he reveal himself which he responds is due to somebody's actions. Elsewhere, Hikaru is found by Art.
Art faces a samurai who possesses the Wind Minimum and steals his powers. Meanwhile, in Nowhere Cafe the Hamatora and their friends reflect on how Art's victims are behaving optimistically as if things improved without their Minimums. Nice compares this being lighter after losing a wallet and remembers how back in Facultas he told Art he wanted to use his money to live a free life. Later that night, Gasquet has a Minimum Holder, Samura, whose works of art force its victims commit murders. Gasquet has to send him to another prison but on their way they are stopped by people discriminating the Minimum Holders. The Minimum Holder then leaves Gasquet's car with a painting covering his halfnaked body that influences the group of people. Nice and his friends prepare to stop the face as Honey predicts the arrival of Art but suddenly suffers amnesia. When Art appears, he covers Samura in water to stop his powers and confronts Nice. Murasaki, Birthday and Ratio interfere forcing him to retreat. Later, Gasquet's new partner is revealed to be a traitor who leaked Samura to an unknown party simply referred as Saikyo.
Nice and Murasaki take two job requests from Koneko to investigate the recent kidnapping of college girls and another by Shinji Toyosaki to protect a safe from thieves. At the same time, PIs Birthday and Ratio head off on a bodyguard request to protect a client. With help from Art, Nice deduces that the kidnappers were targeting the girls for information and theorizes that their cases may be linked. Nice then calls Birthday and Ratio for confirmation just as they are attacked by a Gravity Minimum Holder who forces their client, Azuza to reveal a code. Afterwards Azuza reveals that she and her college friends had been seeing the somniloquous Toyosaki patriarch from whom she accidentally learnt the code. Realizing that the kidnappers and thieves are the same group after the safe Nice, Ratio and Birthday head over to the Toyosaki mansion just as the thieves make their move. While Ratio and Birthday take out the thieves, Nice shows up during Murasaki's stare-down with the hired Gravity Holder and defeats the latter with his Holder ability. Afterwards, as the police and Art apprehend the thieves, the latter contemplates on telling Hamatora of a serial murderer targeting Minimum Holders.
Nice and his friends are shocked to read Hajime's farewell card to him and go to search for her. At the same time, Ratio continues searching a Holder able to heal Birthday who has been hospitalized. He discovers Chiyu in a car and takes her to the hospital, having realized she lost her Minimum. Nice and Murasaki are contacted by Momoka through phone and are lead to a bomb set to explode alongside a person precious to them. While Nice and Murasaki stop the bomb, the person they save is Master. Momoka then shows them two other hostages: Koneko who is in Nowhere and Hajime who is with the Freemum. Nice and Murasaki split to search for their friends. Nice encounters Ratio whose objective, the healing Holder, is in the hands of Freemum. Momoka has Nice and Ratio fight each other with the winner being promised to get their objective. Although Nice defeats Ratio, he is unable to kill him and the Momoka leaves the Holders alone just as Murasaki reaches them. Freemum then moves to another location alongside Hajime.
Taking advantage of Three's rescue, Moral spreads his followers through the city, murdering people they held a grudge against using their Minimums while Moral's assistant Momoka leaks information about Facultas. During the crisis, Takahiro goes to the Hamatora as there was an outbreak of Minimum Holders in prison due to a group known as Black Cosmos. He requests Hamatora a way to recover his body's normal form but Nice rejects the job Hajime decides to help Takahiro by making him going through a diet while Murasaki aids her despite Nice's reclutance. Meanwhile, society becomes concerned about Minimum Holders. Momoka leaks the address of the people discriminating Minimum Holders to bring them chaos. The discrimination against Holders results in Three and Honey losing the rights to take care of the orphans. Ratio and Birthday go to save their Chiyu who is also being attacked for her powers. Nice decides to contact Art but is confused to see the new items in his office. Nice then spots Moral around while Momoka goes to visit an unknown individual.
Nice tries to confront Art but sideffects of his Minimum leave him unable to fight. Art then escapes with Freemium to their club to discuss an alliance with them. Art plans to become their leader and help them reach freedom and in compensation he requires their help. Meanwhile, Gasquet contacts Ratio and Birthday who also started suffering sideeffects. Three also starts losing control on his own body. While being filmed by Birthday, Murasaki's body is also briefly weakened. Gasquet tries gathering information about Saikyo and he learns about an incident from three years ago involving Minimum Holders who lost their powers and how they did not care about them. Art and Freenium attack a prison for unknown reasons but are confronted by Gasquet. The Holders from Freenium overwhelm the policeman as Nice and Murasaki reach the building. When Gasquet dies in front of them, Nice swears he will stop Art.
After realizing Murasaki is still alive, Nowhere's Master calls for an ambulance so that he will be treated. Murasaki manages to recover but it is revealed he has lost his Minimum ability. Birthday, Hajime, Koneko try conforting Murasaki but end up leaving him with more wounds when accidentally throwing him from his bed and Birthday tries reviving him with electricity. Later, Theo and Rei arrive bringing new glasses to him but end up causing more problems. Honey and Three bring weaponry so that he will compensate for his lack of Minimum. Meanwhile, the people from Freenum appear in the hospital for unknown reasons. When leaving Murasaki, Honey, Three, Koneko and Birthday get lost and become tormented due to a possible ghost. They are saved by Master who reveals the "ghost" are actually the former Minimum Holders Art attacked. Nice later arrives to the hospital, bringing Murasaki his own food to have but ends throwing from his bed like the other people. In the epilogue, Moral's former assistant Momoka approaches Hajime.
Hajime wins a trip to the hotsprings and goes alongside Koneko and Honey. Nice and Murasaki are requested by their new client to track down her boyfriend believing he is cheating on her. Nice accepts the job upon learning they have to go to the same hotsprings. There, the duo finds Ratio, Birthday and Three have also come on their own agenda. The inn is then attacked by thieves controlled by a Minimum Holder able to attract men with his sweat. Feeling insulted by the criminals for dismissing the girls, Hajime fights against them using her Minimum.
Moral takes the form of late Art to answer Nice's phone call and starts acting like him. Later, Nice and Murasaki receive a job where they have to find the manufacturer of a drug that sends people into eternal sleep. Nice and Murasaki go to the area with Theo and Rei who visit the beach. There, Theo has an argument with a gang and decides to settle by competing in a triathlon. Shortly afterwards, Nice takes advantage of Theo's appearance to attract a drugdealer who would take him to the drug's manufacturer. Nice and Murasaki learn the manufacturer has taken his own drugs and is their client's brother. In compensation for being used, Theo requests Nice to participate in the triathlon with him. Before the competition, Murasaki talks with the unconscious drugdealer, feeling related as both as constantly overshadowed by others. In the triathlon, the rival gang has hired Honey, Three, Birthday and Ratio but they are disqualified shortly after the beginning. In the final act, Murasaki joins the rival gang to challenge Nice on a one-on-one while bringing the comatose man to see him fight. Although Nice wins, the drugdealer awakes and starts arguing with his brother. Meanwhile, Moral and his assistant Momoka commence a surgery.
Three goes to an orphanage to take care of kids as he and Honey are removed from the murder case by Moral using the disguise of Art. Nice goes on search of one of Moral's allies but fails to confirm any alligment. He and Murasaki are given the task of capturing Three who is revealed to be a former mercenary. In order to get past the media working near the orphanage, Ratio and Birthday bring Honey to the place by hiding here in fruits. Honey learns from Three he is bringing up these kids in a form of selfpunishment for the people he killed as he believe revenge is not a sin but. An angered Honey decides to join him to make the children learn revenege is not good. In the following night, Nice and Murasaki find soldiers near the orphanage led by a Minimum Holder, Helenlee Masayoshi, who admires Three's past and is disgusted by his current state. While Murasaki and Honey protect the kids, Nice and Three take down Masayoshi who activates a gadget to burn his soldiers and thus the orphanage. Deciding to value the children's life over killing Masayoshi thanks a promise he made to Honey, Three manages to get the orphans out of the burning place. In the epilogue, Moral gathers a group of people to start a revolution.
In a flashback, a young Nice talks with Art and Art's younger brother, Skill, about their wish to see Yokohama from a specific building. Back in the present, Nice and Murasaki contact Master to ask how he knew where Hajime had been held before. Master reveals he is a former member of the Minimum Agency (along with Moral and Doktor) who saw Hajime as too dangerous to be alive due to her powers. Master promised to take care of her and left the group with another test subject, Koneko. Meanwhile, Freemum starts a coup d'état to overtake Yokohama. Ishigami and his allies confront the Minimum Agency led by Doktor. Although Ishigami's allies take the upperhand, Honey and Three intervene to stop the fight. Just as Freemum remains victorious, Art starts killing most of them until he finishes Ishigami, as he was just using them to gather more Minimum Holders. Momoka then releases Hajime who goes to see Nice. Nice and Murasaki try to confront Art, but Nice's Minimum deteriorates his body again. Art then stabs Nice in order to shock Hajime and trigger her Nihilist Minimum. This time Hajime's Minimum covers a wide area in Yokohama and Art starts crying in relief as he finally reached his objective.
The episode begins in a flashback showing Nice, Art and Skill's time in Facultas. When Skill was confirmed to have the potential to develop a Minimum, he was not seen by his friends. Art discovers that Facultas was forcing Skill to use his Minimum to make others receive Minimums regardless of what happened to others. As a result, Skill begged his brother to kill him which he did in shock. Art lost the memories of that event until being nearly killed by Moral. Momoka then revealed Art his brother did not entirely die just as he met him. The episode then moves to the present where Momoka kills herself bored with the world. Nice is revealed to have survived Art's attack. He faces Art in rage because of what he did to Hajime. In the middle of the battle, Skill's battle appears using his Minimum to restore everybody's Minimum. After being defeated, Art jumps from the building in order to kill himself. The next day, Nice, Murasaki and Hajime visit Skill's grave and are approached by Art. Nice punches him claiming that if he commits suicide again he will kill him. In the epilogue, Nice and his friends celebrate Art's return to Nowhere.