Kyuu is a junior high school student who loves mystery and dreams to be a detective. He solves a case while shopping grocery and is told about DDS, a detective school owned by the great detective Morihiko Dan.
Kyuu and the others await their results and get news of bombs planted at DDS while they witness one explosion. Will they stop the other bombs and catch the criminal in time.
Q class is allocated a real case where a pot fell on a person's head but doesn't feel like an accident. All they're left with what looks like a dying message.
Q class casually comes across a murder in the neighborhood where the sister of an actress was killed. The actress was performing at a theatre when the murder happened and there was a maid at home who didn't witness anything suspicious.
Q class visits an artist friend of Katagiri kun who was exhibiting his art work. The artist luckily also has a photographic memory. He gets killed by someone at the exhibition and leaves a unique dying message that only Megu can decipher.
Q and A classes go on a field trip to Kirisaki Island to learn about Kirisaki Jack and the double locked room mystery. Things take a turn when a few students get murdered. A new dark and mysterious character named Ryuu is also introduced.
As the class find Saboramaru san's corpse in the double locked room, they bring out theories to try and solve the locked room mystery and find the killer. Later in the night, the killed taunts them by leaving footprints near their rooms.
Another student is killed in their room and Ryuu solves the double locked room murder. While investigating outside the building, something suspicious is seen through a window and as they reach the room, they seen another student murdered.
Q class splits into two groups and investigates parts of the crime separately. They finally solve the strange case with an unexpected solution and Dan sensei is so proud of them. He then explains the meaning behind 'Q' in Q class.
Ichinose seeks help from her friend Kyuu when a spirit medium appears with a letter from her mother who died in a plane crash. Ichinose is skeptical and Q class participate in the next seance where the medium is mysteriously murdered.
Kyuu and the others have come to a conclusion that it was a well planned murder and they investigate further to crack the case. In the meanwhile, Ichnose's aunt is also murdered and there are now 2 murders on their hands to solve.
The culprits of the murders of the medium and aunt are finally caught and the almost-perfect crime is explained by Kyuu leading to the most sorrowful ending possible for Ichinose and the brothers.
A battle between A and Q classes to see who will end up the final members of Q class. Dan sensei puts them up against each other by recreating a miniature diorama murder scene based on the Kamikakushi village and asking both to solve it.
Q class is sent to Kamikakushi village to solve the mysterious disappearances of people who were "spirited away". A film crew is also visiting to document it and search for the village's treasure and one of them gets "spirited away".
Ryuu finds a clue about the village which might be the reason these murders are taking place. A second murder takes place with the victim being another person in the film crew who threatened to find the village's secret.
Ryuu comes up with the solution to how the spiriting away was performed on one victim. He also suspects the village priest to be the murderer. They try to prove he's the killer by trying to break his alibi but yet another murder happens.
The rest of Q class arrive and also perform some investigations. Kazuma decodes an old document mentioning the Japanese army and bio-weapons. Kyuu then starts revealing the killer and identity of the village priest and the village secret.
Q class encounter a murder on their trip. This time it's a food connoisseur lying dead on a table with a multi-course feast setup. There are 4 witnesses claiming to be the first to see the corpse leading to a challenging case.
Megu invites her classmates and Saboramaru home for dinner as requested by her sister. At the door, they realize the lock has been tampered with by an intruder. They enter the house to investigate and observe some very suspicious changes.
Hongou, a new teacher asks Q class to be disciplined and clean the classroom. The others have things to do and leave it to Megu and Kyuu who discover a hidden door behind a large cupboard and go exploring.
It's the next day after Megu and Kyuu were at DDS cleaning the classroom. Their friends haven't heard from them since the previous day and so Q class and few members of A class together start the hunt to find them.
Megu and Ryuu are sent to an elite school to find out about a person who calls himself "the Collector" who murders students and uploads their 'snuff' videos online for the public to watch.
Megu is kidnapped and watches a student being killed right in front of her. The recording that's online shows the murder as well as Megu tied to a chair. Ryuu and the others have to rush to find Megu before she's killed.
Ryuu finds Megu in an abandoned building along with the student's corpse. Another student gets attacked just before she could reveal a hint. After investigating her room, Ryuu finds who the killer is and puts on a show to capture them.
Megu, Yukihara, and the newcomer Kuniko Touya are sent to help Kyuu and Kinta after they're mistaken as perverts during their case, but the Touya gets molested on the train and the girls have to find the culprit from a huge crowd.
Kazuma's teacher at school is shot by a blow-dart filled with curare (a poison) in a sealed room when Kazuma was right outside and nobody came out the exits. Q class joins and have to solve the mystery of the invisible criminal.
Kazuma figures out the criminal who shot the blow-dart at his beloved teacher by demonstrating how it was done. The reason behind the crime and the identity of the criminal leads to a very emotional ending.
A madman has planted bombs in 3 different locations in the city as per a message from the God of gems. Q class is able to figure out which building has the bomb, but they were unable to find it. Will Kyuu and Megu find the bomb in time?
After a failed murder attempt on Kyuu at the house of the violinists, Ryuu gets stabbed and is rushed to the hospital by Kinta in the middle of a bad rainstorm and he has to get past a landslide.
Class Q is summoned to Jinchu village at the request of a well known politician Takatobi because was threatened. On arrival, they see a concrete cabin looking suspicious and they find Takatobi's corpse in an impossible locked room.
Hisashi is murdered and everyone find his corpse in a fireplace. They find an interesting dying message and decode it to find the murderer. The local detective tries his theory of the locked room but fails. Ryu and Kyu figure out the case.
Q class demonstrate how the locked room murder took place and reveal the dying message and the criminal's identity. After being caught, under hypnosis the criminal tries to kill Kinta but fails. Pluto's presence is also made obvious.
Dan-Sensei visits his best friend and comrade, Satoru Renjo's grave. On their way back men with rifles ambush and kidnap him. The culprits call DDS for a ransom at an appointed time or else the bomb attached to Dan-Sensei will go off.
