Phi-Brain ~ Puzzle of God

Kaito Daimon, an average high schooler is a genius at solving puzzles. Apparently, Kaito went to did a table Puzzle route in his school for some "tests" which was referred on his Device. Soon later, he went to look for the Puzzle Club President to inquire about this puzzle which Kaito found suspicious. While solving puzzles (On the device) given by this unknown person named "Minotaur", he completed all his puzzles, and suddenly, a invitation was sent to Kaito from the device, asking him to challenge the 'Sage Puzzle' in the ruins earlier in the episode scene, and to fulfill Orpheus's Contract, however if he failed to solve this puzzle, he will die. As he entered the route to the ruins together with Nonoha, Minotaur said he will be the one who will be watching him do this puzzle, and that the Sage's puzzle is a barrier with treasure sealed, to which Kaito quickly rejected accepting this gift. The first trial he had to do was solve a Sliding puzzle which was quickly solved by Kaito. The second trial was a start point - to end puzzle, this puzzle which Kaito had been bothered about. Kaito had decided to go to a specific deadend which confused Nonoha, she then decided to run while touching the walls to get them out, however, she encountered a trap which nearly got her done for. Kaito and Nonoha arrived at their destination (the dead-end), and Nonoha realised that there's a different between the pillar alignment compared to the rest she had seen. Kaito notices something that is not right, and got reminded of the puzzle he did in the first trial and asked Nonoha if she had seen a pillar with an axe logo. The pillar was found in front of them, and Kaito pulled down the pillar. A wall broke through and they managed to get to the exit. This is where the prize was kept, Minotaur asked Kaito to go alone, and he saw a Mandala. He touched the picture, and suddenly a golden chain chained his arm. Minotaur then told Kaito to use this golden ring to push his powers to the max his brain can handle. Slowly, water started to flow, hitting the supporting pillars of the ruins, Minotaur said that Kaito is to choose one of the three ropes in order to escape. Nonoha screamed with fear and suddenly, Kaito looked up in a state of shock, and his eyes changed to crimson red. He then solved the Sage's Puzzle.

In his powerful state known as 'Phi-Brain', Kaito manages to solve the puzzle, allowing them both to escape the ruins. Later, Kaito becomes annoyed by a puzzle solver named Gammon Sakanoue, who carries the title 'Galilleo'. As Kaito receives a request to solve another puzzle, Gammon tries to claim it for himself and ends up joining Kaito and Nonoha. The puzzle in question is a life-sized sliding puzzle in which the player must get their car out of the puzzle within a time limit before it is crushed by a falling truck. As Gammon nearly completes the puzzle, the puzzle giver cuts off the ability to move the car they are in, supposedly leaving them with no solution. However, Kaito once again enters his Phi-Brain state and manages to use the other vechiles in the puzzle to push their car out of the way before they are crushed.

Kaito meets a boy genius solver named Cubic Galois, who carries the title of 'Edison' and prefers mathematics other puzzles. He attaches a strange bracelet onto Kaito's arm, which causes his head to hurt whenever he thinks about puzzles. At this time, Kaito, Nonoha and Gammon are called to solve a puzzle, with the city rigged to explode if they fail. Though Cubic tries to make things harder for Kaito to make him give up on puzzles, he soon learns that the puzzle giver is serious about blowing up the city. With less than two minutes remaining, Kaito enters his Phi-Brain state and solves the puzzle with a second to spare. Admiring his skill, Cubic apologises to Kaito and removes the bracelet.

Kaito is given a Sage Puzzle to solve on the weekend, where he is to be partnered with Ana Gram, an art enthusiast who holds the title of 'Da Vinci'. They visit the mansion of a late artist, with its butler revealed to be a Giver from the POG. Kaito and Ana are trapped in a room which will fill with gas if they don't solve the puzzle. Presented with a jigsaw containing various famous paintings, Kaito and Ana work together to solve the puzzle, the treasure of which is a series of paintings the painter dedicated to his wife. Back at school, Kaito and Nonoha are surprised to find that Ana is a boy.

The POG extend an invitation to Kaito, who is accompanied by Nonoha and Gammon, to their headquarters. As the three make their way through the maze to meet with the POG's head, Kaito notices something eerily familiar about the puzzles they have to solve. This particularly holds true to the final puzzle, which is similar to a puzzle that took the lives of Kaito's parents. As Kaito goes berserk at the memory of it, Cubic helps Nonoka snap him out of it by shocking him with her cookies. Since this causes Kaito to pass out, the mysterious POG head cancels the meeting. After Kaito recovers, he finds himself having trouble solving even a simple puzzle.

Kaito is still tormented by his memories and unable to solve puzzles. Cubic researches into the Orpheus bangle, theorizing Kaito's breakdown was a result of his brain power being completely controlled by emotions. He advises Kaito to not solve anymore puzzles, as another breakdown could put his life in danger. However, because of a promise he made when he was younger, Kaito can't let puzzles go and accepts another puzzle request from the POG. Kaito soon comes across a complex Kenja Puzzle with Gammon and Nonoha's lives at stake. As Kaito goes through another breakdown, he remembers his promise and manages to regain his puzzle solving skills and solve the puzzle.

As Nonoha visits some kindergarten students, their teacher, Madoka, gives Kaito a letter, which the others suspect to be a love letter. Suspicious about the contents, Nonoha and Gammon follows Kaito to the meeting point, where it's revealed Madoka is a Giver following in her late fiancée's footsteps. Kaito, Nonoha, Gammon and Madoka, along with some children, become trapped in a Kenja Puzzle inside an abandoned building, which wasn't what Madoka expected. Nonoha works to calm the children down whilst Kaito solves the puzzles. When the last puzzle gets destroyed due to falling debris, Nonoha's photographic memory allows her to recreate the puzzle, allowing Kaito, Gammon and the children to solve it, revealing a statue of Florence Nightingale which Nonoha donates to poor children. As a result, Nonoha ends up with the title 'Nightingale', which doesn't exactly please her.

Kaito is contacted by Genius Okudera, a man he once saved from a ruin, who invites him, Nonoha and Ana to a puzzle-themed hotel resort in Hokkaido to solve an alleged Kenja Puzzle being displayed as the centerpiece. After spending a day of activities, Kaito starts to solve the puzzle the next day, becoming suspicious that there aren't any traps involved. As Kaito comes close to solving the puzzle, which he deduces to not be a Kenja Puzzle, he almost succumbs to sabotage but is saved by Nonoha and Ana. Upon solving the puzzle, they find the treasure is a view of nature which has become ruined because of construction of an amusement park. Having painted a picture of what the landscape originally looked like, Ana helps the hotel owner remember the times he spent with his grandfather who created the puzzle, deciding to cancel construction and work on rebuilding the forest.

As Root Academy prepares for a cultural festival, where Kaito finds himself reluctantly entered into a crossdressing contest, the principal, Baron Kaidou, agrees to install a Kenja Puzzle within the academy. Just as Kaito gets into his crossdress, he learns that Nonoha has been taken hostage for the Kenja Puzzle, in which he must eat apples from truth telling dwarves whilst avoiding poisoned ones before the setting burns down. Kaito soon learns from the Giver that granted him Orpheus, who is secretly the student president, Souji Jikukawa, that important information needed to solve the puzzle has been intentionally left out. Souji provides the remaining information for the puzzle, allowing Kaito to solve it and free Nonoha, before getting help from Cubic to save them from the collapsing area.