While solving another Fool's Puzzle, Kaito spots a curious person watching him. The next day, Kaito discovers the school has been converted into a Fool's Puzzle that wasn't arranged by the POG. Finding a strange mirror based "Judgment Puzzle", Kaito meets the person, who challenges him to escape the puzzle or else be killed. Meanwhile, student council member Tamaki Chieno, who has a crush on Souji, is approached by another strange man. As the curious person hints that he knows more about Kaito than he lets on, Kaito manages to solve the puzzle just in time to escape. The man introduces himself to be Freecell, a member of the Orpheus Order who possesses an Orpheus bangle, before Tamaki appears to challenge Kaito to a puzzle battle.

Tamaki, who was given a strange earring by one of the Orpheus Order's members, Pinochle, challenges Kaito to a Judgment Puzzle in which he must navigate an ever-changing maze. Nonoha deduces that Tamaki's change in personality is the result of her earring, which possesses the same properties as the Orpheus bangle. Tamaki uses the power of the earring to increase her brainpower, but Kaito manages to successfully solve the puzzle. As Kaito reaches Tamaki, her earring breaks, returning her to her senses while the Orpheus Order escapes.

While at the arcade, clumsy Puzzle Club member Airi Mizutani is approached by a member of the Orpheus Order, Mizerka, who gives her an Orpheus Ring. After putting it on, Airi suddenly becomes more intelligent and less clumsy. She then lures Nonoha into a trap in order to challenge Kaito to a puzzle where he must solve a crane puzzle in a limited amount of moves in order to save Nonoha. What proves difficult is Airi's stubbornness, as she constantly resets the puzzle every time Kaito comes close to winning. Just then, Airi enters an Orpheus state and brings up a seemingly impossible puzzle before losing consciousness. However, Kaito manages to solve the puzzle, only to discover Nonoha wasn't in any danger at all, while the Orpheus Ring breaks and Airi returns to her normal self.

During the night, the members of the Orpheus Order meetup to receive a message from their leader, Klondike. Meanwhile, as Cubic deduces the recent Orpheus Rings are modernized replicas, Gammon discovers spots Miharu with an Orpheus Ring and confiscates it from her, along with a note directing Kaito and co to a stadium. There, they find the Orpheus Order, who reveal they are using the replicas to collect date for building an authentic ring so they can distribute it across the globe. The Order's secretary, Hoist, then pits Kaito, Gammon, Cubic and Ana in a puzzle match against the Order's Pinochle, Mizerka, Doubt and Melancholy, revealed to all possess authentic Orpheus Bangles, with the losing team becoming electrocuted. In a puzzle to gain the most colored squares, Kaito manages to set things up for Gammon to bring things to a tie so no one gets electrocuted.

Gammon's frustration concerning the Orpheus Order's attempt to target Miharu leads to a slump in the puzzles he makes under his pen name, Setsu Chidou. When he returns home that night, he finds Doubt waiting for him, offering him the chance to join the Orpheus Order. The next day, Gammon asks the POG for assistance and meets up with Elena, who becomes concerned about Gammon's desire to ditch puzzles in favour of revenge. The next day, out of the blue, Kaito challenges Gammon to solve the puzzles he has made, based on the ones Gammon made the first time they met. As he solves them, he remembers his love for puzzles. Afterwards, Gammon sends a letter to Doubt rejecting his offer before vowing to make better puzzles than before, while FreeCell prepares to make a move on Root Academy.

The Orpheus Order show up at Root Academy, revealing themselves to be students of Crossfield Academy, and challenge Kaito and the others to a duel in which, if they win, they will take possession of Kaito. They are brought to their hidden base where they must participate in a team sliding puzzle. Cubic loses the first round against Melancholy, but manages to gather some data to send to Souji. As Kaito prepares for the next round, FreeCell shows off a pendant that Kaito supposedly made a promise on.

Kaito begins his match against Pinochle, who is able to predict Kaito's moves having studies his data, though Kaito manages to turn that aspect against him. Just then, Pinochle begins revealing things about his past at Crossfield Academy, reminding him of a promise he made with Freecell that he broke while searching for Rook that day, which supposedly led to the death of Freecell's mother. With his determination wavered, Kaito ends up losing the match to Pinochle.

As Kaito has some alone time following his match, where he recalls more about his past, Ana talks with Nonoha about his sister, Eve, who helped cheer him up when he was down. As the game resumes, with another loss resulting in a team loss, Ana faces off against Mizerka. As Mizerka becomes annoyed by how much of a free spirit Ana is, Nonoha shows Kaito a chalk drawing Ana drew, based on a painting Eve did for him. Firm in his belief in Kaito, Ana manages to win his round. Afterwards, Kaito gives his thanks to Ana, who suggests he try and do the same thing for Freecell.

As Freecell refuses to tell Kaito the truth about what happened to his mother, Gammon gets Hoist to combine the remaining two matches into a tag-team duel with Kaito and Gammon against Freecell and Doubt. As Kaito continues to struggle throughout the game, Freecell continues to torment him. Just then, Cubic receives the date he had Souji analyse, revealing that Freecell and the others had been consumed by the Orpheus rings, which are controlling their emotions just like Rook was. As Nonoha reminds him of his promise to solve all puzzles, Kaito regains his senses and works with Gammon to win the game.

Following the battle against Orpheus Order, Elena transfers into Root Academy and takes the Phi Brain kids and their friends on a vacation on her private island, where puzzling is forbidden. However, Kaito and the others have trouble relaxing due to the lack of puzzles. They soon get excited when they find a clue to what is supposedly a puzzle and go into a cave to search for it, not willing to listen to Elena's explanation. In the end, it is revealed to be the set of a monster movie the POG made which almost made them bankrupt and was kept a secret. Realising there's no stopping them, Elena turns the vacation into a Puzzle Camp, much to the annoyance of Nonoha.

With the vacation now fully puzzle focused, Nonoha feels like she has nothing to do. Wanting to spend more time with everyone, Nonoha decides to join in Elena's intense puzzle training. Although she sucks at the physical puzzle, she shows talent in solving digital versions of the Kenja Puzzles they faced before thanks to her photographic memory. After feeling a bit more left out, Nonoha becomes determined to solve a puzzle she received from Kaito when she was little before the camp ends. As she focuses on the puzzle, the others seem to get a little less enthusiastic. On the last day of the camp, Airi and Miharu come to Nonoha for help with preparing breakfast. Afterwards, Nonoha realises she still has a place to belong to even without puzzles.

As Rook and Bishop investigate the Orpheus Order elsewhere, Souji expresses his desire to quit both the student council and the puzzle club. Meanwhile, Souji is contacted by Minotaur, who is revealed to be working for the Orpheus Order and tries to tempt him with a replica ring, though he still refuses. The next day, Naoki Takeda decides to run for student council president, prompting Tamaki to run against him. Later that day, Souji receives an invitation from Minotaur to come to the place where Kaito found the Orpheus Bangle, challenging him to a Fool's Puzzle which would destroy the academy should be lose, presenting him with a replica ring so he can solve it. As the others get word of this, Cubic reveals what Souji told him about willingly becoming a labrat for the replica rings. As they arrive on the scene, they find that Souji had solved the puzzle using the replica ring and challenges Kaito.

Souji sets up a sliding puzzle for Kaito, also threatening to blow up the academy should he fail. As Cubic, defiant that Souji hasn't changed, goes to search for said bomb to prove his theory, Nonoha and Ana end up helping Tamaki with her paperwork in order to get her to evacuate. As the game progresses, Souji soon feels the advantage of the replica ring and starts to enjoy it. However, Kaito soon expresses his joy at such a fun puzzle and turns it around for the win, which leads to the replica ring being destroyed. Afterwards, Souji explains what he had learnt from wearing the ring, deducing the rings will destroy themselves if their user feels they have lost. The next day, Tamaki is voted student council president whilst Souji goes on a journey, leaving Kaito with another truth he discovered about the rings; their desire to join with him and become true Orpheus Bangles.

Elena is told off by Tamaki after makes various 'improvements' to the school without permission. Meanwhile, former POG member Herbert Muller appears before the Orpheus Order, beating Doubt in a puzzle and revealing he has a genuine Orpheus Bangle. As Hoist decides to tell Freecell the intentions of their leader, Klondike, Herbert kidnaps Elena to lure Kaito and Nonoha to a film studio, where they must both battle against two Orpheus Order members, Wu and Noh, in order to rescue Elena. As Nonoha struggles to keep up, Rook shows up to take her place, along with Bishop who rescues Elena, allowing Kaito and Rook to beat the puzzle.

As Melancholy takes interest in a girl named Lotte and her intelligent dog named Rummy, Rook shows Kaito and the gang a newer Replica Ring model recovered from a manufacturing plant for Cubic to analyze. Melancholy equips Lotte and Rummy with Replica Rings and uses them to confront Rook in a puzzle, in which they must navigate a fog filled maze over a deadly drop, with the loser falling to his death. As Rook manages to learn the trick to solving the maze, Rummy struggles under the command of Lotte, whose personality is manipulated by the Replica Ring. As Rummy stops, Rook reminds Lotte that it's not the mazes Rummy liked, but her. As Herbert decides to set the maze to automatically collapse, Rook manages to reach the center in time to save both Lotte and Rummy. The next day, Rook returns to the POG to help stop the Orpheus Order from claiming more victims.

Ana is visited by his older sister, Eve, who is soon revealed to possess an Orpheus Bracelet, showing a drastic change from the kind-hearted personality that Ana admired and blaming him for having to give up her dream as a painter. Working with Mizerka, she challenges to Kaito to game where, should he lose, Mizerka would break Ana's arm and end his dream as a painter. Kaito is tasked with completing a large picture puzzle in fifteen minutes. As Eve laments how she suffered due to Ana overtaking her in artistic talent, Kaito manages to complete the puzzle, revealing a painting of suffering that Eve drew. After Kaito explains how neither the puzzle or the painting represents the true Eve, Mizerka attempts to attack Ana but Eve stops her and her bracelet, which turns out to be a Replica Ring, collapses. As Mizerka contemplates how Eve was used an experiment, Eve goes under the protection of the POG, although Ana feels she is lying when she says she'll take up painting again.

Pinochle challenges Kaito to a puzzle, saying he will tell him everything about what happened between him and Freecell should he win. However, the loser will fall into a furnace. As Pinochle tells of how Kaito was supposedly a liar, Kaito simply states he wants to know the truth so he can properly apologise for what he may have done and soon makes a comeback. As they reach the top, Kaito refuses to finish Pinochle off, as hurting someone for the sake of a friend is not something that friend would appreciate. As Whist sabotages the puzzle to try and make Pinochle fall, Kaito manages to use his smarts to rescue him. As Pinochle realises what he wants is to become true friends with Freecell, his Orpheus Ring breaks, revealed to be another Replica Ring. As Freecell and Whist tell the others that Pinochle died, Pinochle reveals that he spread bad rumors so that Freecell wouldn't become friends with Kaito and abanadon him, with Cubic deducing that the Ring caused him to believe in his own memory that Kaito did it. As Pinochle mentions he doesn't know the connection between Kaito's promise and the death of Freecell's mother, Kaito decides to become friends with him.

After finding out the location of Orpheus Order's hideout from Pinochle, Kaito and the gang head there, where they are confronted by Herbert, who is wearing two rings. He challenges Kaito to puzzle in which he must use a boat to ferry everyone across to the other side whilst taking into consideration roles they have been given, with Kaito requesting to meet with Freecell should he win. Things get a little complicated when two necessary keys are thrown into the mix. Despite some last minute interference by Herbert, Kaito manages to solve the puzzle. As Kaito commends Herbert on his puzzle, he becomes possessed by the rings and activates a bomb against his will, causing the puzzle room to collapse with Kaito and Herbert inside it.

As Cubic works to help Gammon and Ana, Nonoha goes in search of Kaito and comes across Freecell. After some reluctance, Nonoha accepts Freecell's help in solving the puzzle blocking their way to where Kaito is, being given a memento from his mother as payment. As Freecell tells Nonoha about how he feels Kaito's broken promise is related to his mother's death, his Orpheus Bangle glows a mysterious color and his memory is rewritten, leading him to now believe his mother's death wasn't Kaito's fault, but his own. As the cave soon begins to collapse, Freecell uses the power of his bangle to solve the puzzle. After managing to find Kaito and Herbert and getting them to safety, Freecell reveals the Replica Ring he had been wearing had evolved into a true Orpheus Bangle, challenging Kaito to a game when he is ready.

As the gang try to figure out more behind Klondike and the Replica Rings, Cubic reveals to Gammon that Kaito's brain patterns are still accelerating even without the Orpheus Bangle. Meanwhile Kaito, who had a vision involving Freecell and Nonoha, is approached by Whist, who reveals all the rings the Orpheus Order wears are replicas, but Freecell had managed to use it to awaken as a Phi Brain child. Realising he needs to become stronger, Kaito asks Rook to take him to a Fool's Puzzle. Kaito is soon brought to a maze where he must carefully avoid statues which trigger trapdoors. Managing to reach the end of the puzzle safely, Kaito discovers that Freecell had managed to solve it first. As Rook decides to help Kaito train against harder puzzles, Freecell meets up with Whist, revealing what he now knows thanks to the Ring.

Mizerka and Doubt are sent a password to access their confidential files, where they learn the truth about their rings. As Mizerka learns Melancholyhad been playing along with her the entire time, she and Doubt get their rings upgraded by Doubt and go to challenge Kaito and Ana to a final puzzle. Baron agrees to the challenge and has Gammon construct a collapsing construction site puzzle to battle on. As the puzzle goes on, everyone takes after Ana's example and enjoy the puzzle. As Kaito gets into a winning position, Mizerka expresses her desire to live, and both her and Doubt's rings break, although they are both rescued. Afterwards, Pinocle reveals he was the one who sent Mizerka the password so they could be saved. Meanwhile, Freecell meets up with Orpheus Order's leader, Klondike.

Melancholy and Whist appear at the POG headquarters to deliver a message from Klondike challenging Kaito to a puzzle, revealing he has Freecell in his possession. As Kaito and Klondike prepare themselves for the puzzle, in which they must design a maze for their opponent and be the first to solve their opponent's maze, Klondike reveals all of his experiments were to create a Final Ring for himself. As Kaito struggles against Klondike's maze, Melancholy reveals her ring is a genuine Orpheus Bangle. As Kaito figures out the nature of Klondike's maze, Klondike activates his Final Ring, absorbing Kaito's brainwaves to complete it.

Souji returns having been to Crossfield Academy where he retrieved a diary from someone who used to be in the Orpheus Order. It details how the Orpheus Order was changed when Klondike decided to have the Orpheus Ring examined in order to make replicas. The first prototype ring was worn by the diary's owner, a woman named Solitia, who is revealed to be Freecell's mother. Believing the rings to be dangerous, Solitia fled the Orpheus Order with Freecell, chronicalling the effects the ring had on her in her diary, which she was unable to give to Freecell before she passed away. As Kaito becomes determined to rescue Freecell from his fate, the POG and ex-Orpheus Order members instigate a plan to stop Klondike and destroy the Final Ring. Hacking the elevators, the POG manage to bring Klondike, Whist and Melancholy to a dead end, where they are confronted by Doubt and Pinochle. However, Klondike manages to foresee this and escape to the roof where Freecell awaits, demonstrating a power that frightens Melancholy to the point of her Orpheus Ring breaking. After Freecell manages to overwhelm Klondike somehow, he heads off on a helicopter, leaving a message to Kaito to meet him at the location of God's Puzzle.

As Freecell becomes curious as to why Nonoha is present in a vision of him facing off against Kaito, Kaito and the others ponder why Freecell needed Klondike's Final Ring. The next day, Hoist abducts Nonoha, taking her to Freecell's location in the Himalayas. As Kaito and the others head to their location, Freecell explains how the memento he received from Solitia was a puzzle he wanted to solve with Kite. Nonoha then proceeds to tell him the truth about what happened to Solitia. She also manages to replicate a puzzle Solitia made containing a secret answer showing Solitia's earnest feelings for Freecell, who then starts envisioning Nonoha as his own mother. Meanwhile, Kaito and the others are greeted by Hoist, who wants to create a successor that can surpass God.

Kaito and Freecell begin the puzzle in which Kaito must use clues to chase down Freecell. As they constantly try to outwit each other, their brain levels increase and they soon start running in circles without end. As they both start to reach their limits, Nonoha calls out to Kaito and snaps him out of it, allowing him to end the eternal loop and solve the puzzle. Despite the puzzle being solved, Freecell remains soulless as his ring is still active. Remembering Freecell's original promise with him, Nonoha gets Kaito to help Freecell finally solve his mother's pendant, allowing him to break free of the ring and return to normal. As Freecell and the others return to Crossfield Academy, Kaito and the gang resume their duty of releasing the Fool's Puzzles.