Whilst exploring a Sage's Puzzle in England with Jin in the hopes of recovering his memory, Kaito stumbles upon an unsolved puzzle, having assumed Jin had already solved all of them. Solving the puzzle with ease, Kaito discovers a brooch with a cat engraved on it, which Jin takes an interest in. Later, they, along with Nonoha and Rook, go to the Fool's Puzzle where Kaito and Rook previously faced off against each other, where they encounter a strange girl named Raetsel, who takes the brooch and runs off with Jin inside the puzzle, activating its traps. Back in Japan, a man named Johan Seigmund Enigma appears before the other Phi Brain children, attaching an explosive puzzle on Cubic's back, stating his intent to annihilate all puzzlers, claiming it to be Jin's desire. After the bomb is disarmed, Enigma leaves whilst his accomplace, Whodunnit, challenges the others to a puzzle. Meanwhile, Kaito's group arrive at a room with many doors, with Raetsel tasking them with finding the correct door before the ceiling collapses, claiming that Jin hated puzzles.

Thanks to Kaito's deductions and Nonoha's memory, their group manages to find the correct exit and escape. Afterwards, Raetsel takes everyone to her personal boat, where she shows them a feed of Gammon's group as they face Whodunnit's puzzle, where they must arrange cubes successfully or else be electrocuted. Working together, they deduce the colors of the cube are a clue to numbers in a magic square puzzle, managing to solve it with a second to spare. Although Raetsel leaves Jin with Kaito and the others, they are left uncertain by how the Master Brains, who target puzzlers for bounty rewards, claim to be contracted by Jin.

As Raetsel transfers into Root Academy, Gammon spots Jin behaving rather oddly, uncertain whether or not to believe either Kaito or Ratesel. Later, a Master Brain posing as Jin appears before Kaito, challenging him to a Fool's Puzzle in which he much navigate a sliding puzzle maze within a time limit or else fall to his death. As Kaito comes close to solving it, the fake Jin blows out one of the rooms, preventing him from reaching the exit, as well as tilting the maze. However, Kaito manages to take advantage of risky nature and reach the maze's goal in time.

Whilst Kaito is having a picnic with Jin and Nonoha, Raetsel appears before Kaito, stating that the Fools' Puzzles made Jin suffer, clashing with Kaito's own memories of him. However, Nonoha helps them realise there are some memories of Jin that they both share. Meanwhile, a Master Brain named Dr. Theorem appears before Cubic, who decides to face him in a puzzle to prevent him from reaching Kaito. Cubic is tasked with finding 'the most beautiful number' within 15 minutes before he is engulfed in flames. After Kaito learns of Cubic's predicament, he rushes to his aid and helps him find the solution; the golden ratio. After the battle, however, Jin starts experiencing pains in his head.

Jin once told Rook that “Puzzles are chains. Puzzles are also mirrors.” Unsure how to interpret those words, Rook jumps on the chance to challenge a Puzzle of Fools that Jin once fought in the hopes of gaining insight into his heart...

Gammon is about to blow a gasket when he learns that he has the lowest bounty now. He’s desperate for a chance to boost his bounty, but he may have gotten more than he bargained for when Demolition Man challenges him to a puzzle battle.

Bent on vengeance, Melancholy becomes a Master Brain. Freecell wants to leave the world of puzzles behind, but Melancholy won’t let him as she drags him into a Puzzle of Fools. Can Kaito and Gammon save him?

After escaping from Jin’s Puzzle of Fools, Melancholy invites Kaito and his friends over to her house. Freecell hopes to use this unexpected opportunity to mend their relationship, but he has a long and bumpy road ahead of him...

Enigma makes revelations about Jin's past and explains the connection that Raetsel shares with Jin.

The puzzlers arrive in Texas after following a clue left behind by Raetsel. Gammon rides to the rescue as he solves a puzzle that is managed by a misguided brother.

Ana and Cubik have decided to help Kaito solve Raetsel’s puzzle! Whenthey reach the coordinates Kaito gave them, they discover that Kaito and his group got caught up in some bad weather. Can they find the next clue on their own?

Herbert is bent on defeating Kaito in a puzzle battle. He’ll do anything it takes to taste sweet victory, even if it means using the power of the Rings. Can Kaito and his friends defeat the ultimate king of cheaters?

Raetsel has decided that it is time to face Kaito personally. She’s convinced that the “something” she’s lacking is “determination.” So she’s ready to go all out! But if she’s not pulling any punches, why is her puzzle so easy...?

Rook and Freecell must go all out if they hope to free Raetsel’s puzzle. Souji has returned from the Republic of Amgine, bringing back stacks of confidential information. Can Baron use the information to figure out who Enigma truly is?

While the Baron is revealing Jin's past and his ties to the fallen puzzler Lavoushka. Enigma shows up and reveals his past and his motives for having the puzzlers eliminated

Nonoha and Kaito break the truth to Raetsel, both about Jin as well as about Enigma. But will that be enough to finally win her over? If Raetsel decides she doesn’t want to share Jin, there’s only one way to duke things out... with puzzles!

Orpheus has been resurrected! He wants to become the perfect Phi-Brain, even at the cost of mankind. But first, he needs a new vessel. He offers Jin’s life in exchange for the life of a Phi-Brain, but will anyone take the bait?

Orpheus shows Kaito, Nonoha and Freecell what altering the past could entail. He promises that this power will be theirs if they become Phi-Brains and offer their bodies to him for a short period of time. Will they submit to temptation...?

Upon learning that Jin could be saved if someone else replaced him as the Orpheus's vessel, Gammon and Erena go to the Republic of Amgine to challenge Orpheus once and for all.

Raetsel accepts Orpheus's puzzle challenge only when he promises to bring back Jin.

Fed up with waiting around for Orpheus, Kaito accepts the challenge and is inadvertently dropped into a puzzle to face a close friend.

The puzzlers are pitted against each other in a game that will test their puzzle solving skills and their camaraderie.

The Puzzle of God begins tomorrow! Kaito and Raetsel are both eager to face the puzzle, but one of them seems ready and one of them doesn’t. Raetsel has a blast partying the night away with the girls.

In the Puzzle of God, Kaito and Raetsel must travel through their pasts and alter them. However, they must be careful not to let the puzzle consume them. If it does, they could spend all eternity wandering the Time Maze!

Kaito and Raetsel reach a turning point in their battle to solve the Puzzle of God. To solve this puzzle they must resort to unforeseen tactics.