Kaito Daimon is a puzzle solving machine. So much is his mastery over all that is perplexing, that he suddenly becomes entwined in a lethal game of Riddle Me This. The contender? A deadly Philosopher's Puzzle, the creation of a sinister group named POG. Along with his "friend" Nanoha, he is pulled into a world of mysteries, where failing to find the solution could mean taking his last breath. Solving the puzzle is only the beginning of Kaito's problems in Phi Brain ~ Kami no Puzzle!
Mysterious ruins are never a sign of good things to come. Kaito and his friend Nonoha discover a strange puzzle while exploring the area and not solving it right could mean the end for both of them!
With his new found powers, Kaito must now go face to face with another Solver who goes by "Galilleo". Things get worse when Galilleo claims Kaito's new puzzle request as his own.
Racking your brain just took on a whole new meaning. A new Solver has attached a bracelet on Kaito that causes headaches whenever he thinks about puzzles. Kaito's powers are no use here, so he'll have to find another way to win against this crafty boy genius.
Time to partner up! Kaito is given a puzzle to solve with some help from "Da Vinci", an art enthusiast. While visitng the mansion of a late artist, they both become trapped in a room. Gas is seeping in, time is running out, and the pressure's on for this Solver duo to figure it all out!
The mysterious organization known as POG invites Kaito to their headquarters. Along with Nonoha and Gammon, Kaito makes his way through eerily familiar puzzles, until stumbling on to a puzzle that brings back memories he'd rather forget...
With the Orpheus bangle still tormenting Kaito and keeping him from solving puzzles, Cubic takes a stab at researching the bangle to find an answer. The temptation is too much for Kaito, and he attempts to figure out one more puzzle even if it endangers his life.
While Nonoha visits kindergarten students, their teacher hands Kaito a letter. Suspicious of the contents of the letter, Nonoha and Gammon follow Kaito in hopes of finding out the truth. What they do end up finding is another deadly puzzle, and it falls on Kaito to save them before the worst happens.
Kaito, Nonoha and Ana are invited to spend the day at a puzzle themed hotel. This is no ordinary vacation, however, as the hotel holds within it a puzzle with no traps, which makes Kaito think that there's more to it than meets the eyes.
While Nonoha is taken hostage, Kaito finds himself competing in a cross dressing contest.
Kaito and company find themselves trapped in another Kenja puzzle. Kaito is given the option of sacrificing his friends to get hints, while Gammon and Nonoha are given the same option.
Elena asks Kaito and his friends for help as extras in a new show she is starring in. Later, Elena introduces them to a new Kanja puzzle. A 3D puzzle is three times as deadly, and Kaito must solve it before the shocking finale!
Kaito crosses paths with Rook, a childhood friend and head of POG Japan and learns that he is to become an exchange student at Crossfield. While reminiscing about old times, they discover a path that leads to a new Kenja Puzzle...
With the discovery of the Kenja Puzzles known as "Fool's Puzzles", the entire game changes. With Rook in Danger, Kaito desperately tries to push through the puzzle, knowing full well what awaits him at the end.
With Kaito sidelined in the hospital, Cubic takes up the role of puzzle king when an invitation by Rook presents a chance to prove his loyalty. A military themed POG puzzle awaits, and failure to solve it will have Cubic looking down a tank's barrel!
Kaito, becoming frustrated with Rook's attitude toward Cubic, makes his way to one of Rook's old apartments. Along with Nonoha, they learn more about the enigmatic Rook. Meanwhile, Ana's investigations lead her to a new puzzle in some familiar ruins.
POG has taken over all planes leading to Japan, so Kaito and co. get re-routed to Venice. While discussing the Phi Brain project, Gammon figures out the truth behind the reason they're in Italy. A new puzzle awaits!
The mysteries continue as Kaito and the others return to Japan, only to find that their school principal is missing. Later, Kaito is lead by POG to the place where his parents died, and one more piece is added to the puzzle of his shrouded past.
The atmosphere at Genius Tower has become...strange. With Kaito contemplating the fate of both Rook and POG, Nonoha's at her wit's end trying to cheer him up. A summons from the principal to Gammon and Kaito, however, quickly brings him back to Earth.
Miharui is worried. She hasn't heard from her brother Gammon in some time, so she goes to Kaito for help. Gammon, meanwhile, is headed to POG Headquarters, desperate to find any sign of Rook.
Kaito and Gammon square off in a deadly puzzle, with an item known as the God Scrolls in Gammon's cross hairs. The scrolls are needed to complete the Puzzle of God, but Kaito is once again shown a terrifying vision, just when victory is within sight...
Kaito has suddenly begun losing his focus when looking at puzzles. Cubic reveals that Kaito's brain has sped up to abnormal levels, causing loss of focus. Kaito, however, isn't going to let something like this keep him from solving another Fool's Puzzle.
With Jin now a complete wreck, Gammon finds out that POG's leader, Count Pythagoras, intends to pit Kaito and Rook against each other in order to open the gate to the Puzzle of the Gods. The race is on, and everyone has a chance to be first.
After his encounter with Rook, Kaito visits Ana, whose drawings resemble what he sees in his visions. Afterwards, Gammon challenges Kaito to a puzzle in which they must climb ever upwards to win. The catch? Trying not to get crushed by your opponent.
As POG rips at the seams after Rook's revelations, Kaito is contacted by him, with an offer to spend some time together...with a surprisingly friendly demeanor. What could Rook be hiding? A fight to the death looms, and only one can come out alive!
A menacing new puzzle awaits Kaito, with Rook in the center of it all. With the God Scrolls on the line, Kaito must solve this strange new ball puzzle fast, while also saving Rook from himself.
Looks like Kaito has an admirer...or perhaps a stalker? While solving a Fool's Puzzle, he notices someone watching him intently. What's worse, it seems that the entire school has turned into a giant Fool's Puzzle as well.
Tamaki, outfitted with the strange earring given to her by an Orpheus Order member, throws down the gauntlet and challenges Kaito to a Judgement Puzzle. Something seems to be a little off about Tamaki, however, and Nonoha may know why.
Clumsy people are the most likely to fall into some trouble, as is the case with Airi Mizutani, a Puzzle Club Member who runs into Mizerka. An Orpheus Ring is offered. What kind of trouble will arise when a klutz like Airi dons the ring?
Members of the Orpheus order are gathering to receive a message from their leader, Klondike. Gammon spots Miharu with an Orpheus Ring, and Cubic is closing in on an answer to the Orpheus Ring dilemma, while Kaito and Co. are invited to a stadium.
Gammon's puzzle production under his pseudonym "Setsu Chidou" is slumping, due to his concern over Miharu and the Orpheus Order's attempts to target her. Later that night, a strange, yet tempting offer is presented to him by Doubt.
The Orpheus Order appears at Root Academy, and reveal themselves as Crossfield Academy students. A duel is proposed, with Kaito as the prize for the victors.
Kaito and Pinochle begin their match, but Pinochle has an advantage: by studying Kaito's move data, he is able to predict what he'll do next! How will Kaito overcome such an overwhelming tactic?
Kaito reveals more about his past following some down time after a match. Ana and Nonoha discuss Eve, Kaito's sister who helped pick him up when he was down, and who will play an important part in the battle to come.
Freecell outright refuses to tell Kaito about his mother. Gammon works his magic and manages to combine the last two matches into a tag team duel, with himself and Kaito against Freecell and Doubt.
After the grueling battle against Orpheus, Elena transfers to Root Academy and invites Kaito and friends to her private island. They soon discover the beginnings of a puzzle. There's just one catch: on THIS island, puzzle solving is forbidden!
With the vacation puzzle at its end, Nonoha has suddenly found herself with nothing to do. Wanting to spend more time with her friends, she decides to join Elena in puzzle training.
Minotaur has returned, and is impressed with Kaito's ever evolving abilities. He has created a new game just for Kaito, and lures him in with the promise of revealing the secrets behind the true Phi Brain.
Souji steps up the pressure, presenting Kaito with a sliding puzzle that he must solve. The school is literally on the line: failure to solve this puzzle will cause the Academy to explode! With Kaito busy, Cubic is on the hunt for the bomb.
After a whirlwind of unnecessary improvements to the Academy, Elena is berated by Tamaki for being irresponsible. Meanwhile, a former POG member returns and appears before the Orpheus Order, bearing a familiar and troublesome item.
Lotte and her intelligent dog Rummy have piqued Melancholy's interests. Meanwhile, Rook shows Kaito and Co. a newer Replica Ring for Cubic to analyze. Melancholy uses the rings to challenge Rook to a puzzle, with Lotte and Rummy as her pawns!
Ana is suddenly visited by Eve, his older sister and possessor of an Orpheus Bracelet. Her drastic change in personality can only be attributed to her new accessory, and Ana is hoping that Kaito can somehow break the spell.
Pinochle challenges Kaito to a puzzle, and is willing to tell him that transpired between himself and Freecell. The loser, it seems, will be thrown into a furnace.
After Pinochle divulges the location of the Orpheus Order hideout, Kaito and his friends make their way there, only to be confronted by Herbert, who is now in possession of two rings. The classic ferry boat puzzle is the challenge, and Kaito is more than willing to crack it.
While Cubic works to aid Gammon and Ana, Nonoha goes off in search of Kaito. She stumbles upon Freecell and reluctantly agrees to accept their help in solving the puzzle that will lead her to Kaito.
Looking to train against harder puzzles, Kaito asks Rook to take him to another Fool's Puzzle. Cubic reveals to Gammon that Kaito's Brain patterns continue to accelerate, even without the Orpheus Bangle.
The truth about Doubt and Mizerka's rings is finally revealed. Betrayal leads Doubt to upgrade their rings and challenge Kaito and Ana to one final puzzle. A collapsing construction site is the battlefield, and all players are ready to fight!
A letter of challenge from Klondike to Kaito is delivered to POG HQ by none other than Melancholy and Hoist. With Freecell in his possession, Klondike aims to best Kaito in a maze building puzzle.
Souji returns to Crossfield to retrieve a diary that used to belong to a member of Orpheus. Within it lies the details of how Orpheus was changed once Klondike began to study the Orpheus rings.
Nonoha is kidnapped, and Freecell seems to be pulling the strings, curious as to why she shows up in a vision of himself going up against Kaito. The Himalayas set the stage for a final battle, while Kaito and his group rush to save Nonoha.
The final puzzle is at hand! Kaito and Freecell are in a frantic race to outwit each other at every turn, and in the process begin taxing their brains past the breaking point. With no escape from their mental loop, Kaito is in danger of losing Freecell, as well as himself.
As Kaito tries to help Jin solve his memory problems, a young woman named Raetsel steps in to take matters into her own hands.
Raetzel reveals that the Republic of Amagine has a bounty on every last puzzlers heads.
With the puzzlers confusion heightened, an imposter makes an attempt to put an end to Kaito's puzzle solving.
The great mathmagician Dr. Theorem challenges Q-Taro to an illogical game of numbers.
With the help of Kaito, Rook takes on a deadly puzzle of fools in order to uncover Jin's past.
While the girls take Raetsel on a girls day out they find themselves the victims of a master brain's trap. Gammon, looking to increase his bounty, accepts the master brain's puzzle challenge and frees the trapped victims.
While Kaito learns that Jin may have created three puzzles of fools, Melancholy exacts her revenge on Freecell by becoming a Master Brain herself. Freecell needs the help of Kaito and the other puzzlers to get out of the explosive place he is in.
Having been tricked by her boss, Melancholy and the other puzzlers banned together to solve the puzzle of fools. Once the puzzle is solved, they all meet at Melancholy's family estate to try and make amends with her.
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.
Cubik and Ana are waiting for the other puzzlers to arrive when they meet a woman named Regina who offers to take them on a mini tour of the water falls that is sure to make a splash.
Herbert Mueller is determined that the puzzles he has created will defeat Kaito and the Puzzlers for good.
Determined to defeat Kaito, Raetsel sets out to create a puzzle that even the best cannot solve. Half way across the world, Rook discovers the entrance to Pythogoras's puzzle which may hold clues to recovering Jin's lost memory.
Kaito and the other puzzlers complete their puzzle only to discover that half way across the world, the puzzle that Rook and Freecell must solve is their only escape. Will Rook and Freecell succeed and also receive the prize they were after?
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.
Kaito and Nonoha reason with Raetsel by revealing what Enigma has been hiding. With the truth finally revealed, Raetsel is still determined to be the one to bring back Jin's memories.
After Jin regains his memories, the Phi-Brain Orpheus reveals himself in Jin. Kaito and the puzzlers re-group at the POG head quarters and are briefed by Rook and Freecell about what has just happened and how they can save Jin.
Kaito, Freecell, and Nonoha learn that they may be able to alter their past if they listen to Orpheus and become his vessel.
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.
Kaito locks himself in his hotel room to reflect on the outcomes of the last few puzzles he has solved. Raetsel gets him out of the dumps and decides that the best way to defeat orpheus is to work together.
Kaito and Raetsel face a reality that could have been while they work towards a solution to the Puzzle of God.
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.