In Egypt Isis learned of Seth's reincarnation as Seto. She decided to give him the remaining god card Obelisk in the hopes that he could help her defeat her brother and return things to how they were before. She told him of his past as the priest, but Seto didn't believe it. He still set up a tournament to win the other god cards, deciding he liked them and enjoying the chance for another contest against Yugi. Malik and his gang of rare hunters followed Isis with plans to get the final card and finally have his revenge for his past. He's surprised to learn that the pharaoh's awake, and possesses Keith using the Rod to steal the Puzzle. With the Puzzle taken from Yugi Yami is forced back inside. The shadows immediately act on the opening to attack Yami and strip him of his new memories and sense of self. Yami holds on, hoping Yugi will get the Puzzle back quickly before he begins to lose his memories again. Malik quickly challenges Yugi to a duel through Keith, as the ownership of an Item can't change unless it's won or given away, with the plans to destroy the Puzzle once it's his. Yugi agrees and initiates a shadow game to Malik's surprise. Marik tells Malik that individuals can use magic if strong enough, but Yugi can only use Light magic as he has no Dark.
Malik believes that by combining Light and Dark magic he could win, but the distance between them and their puppet doesn't allow them to put their plan into action. Yugi wins, but Marik has Keith smash the puzzle and set the place on fire, furious at the other's success. Shattered Yami finds his newborn humanity rapidly being torn away from him as he no longer has a solid anchor he can use to fight from. Yugi's friends are worried when they realize that Yugi has gone missing, knowing the Puzzle tends to attract trouble. Bakura hears and uses his Ring to track Yugi down. He helps Yugi gather the Puzzle pieces and assemble it, sealing a part of himself into the Puzzle in hopes it will help him when he goes to take the Item later on. He leaves before the others arrive. They manage to rescue Yugi after the Puzzle is rebuilt, much to their dismay at his stubbornness. Yami reveals what happened while in the Puzzle, and confesses that he thinks he might have been human once. Yugi agreed to help him learn about his past.
Yugi sets Yami and Tea up on a date together as he trusts Tea as his closest friend to be able to help Yami. It doesn't go well, as Tea is rather nervous, and Yami still isn't used to modern society, but they do get better with each other and Yami slowly relaxes regaining a fraction of what he lost while in the Puzzle again. Their day's interrupted by a guy demanding that Tea cheated at DDR and trying to beat her. Yami interferes and turns the DDR into a shadow game, and destroys the man. Tea realizes that Yami doesn't see it as wrong, and struggles relaxing again as she realizes just how far Yami is from being normal. Yugi ends up having to comfort Yami's sorrow over Tea's reaction, a little amused as Yami is actually much better than he had been before. The day ends with the pair at the museum looking at an exhibit. They're shocked to find a tablet displaying what looks like Yami and Seto dueling with Blue Eyes and Dark Magician in an ancient Egyptian tablet. Isis is there working at the exhibit to allow her to keep an eye on Seto and the pharaoh, and is extremely excited to realize that the pharaoh she was raised to serve is in the museum. She explains Seto and Yami's past using the Necklace to show them the past. Yami learns he was a pharaoh for sure and can no longer deny it, and Seto a priest. Even more, they were cousins to his surprise. Yami feels closer to Seto with this knowledge, but he doesn't want to be a pharaoh. He's just barely human like now. Yugi agrees he'll help Yami find a place in this time, pleased that Yami now wants to be more human. Tea confronts Yugi about Yami's behavior, shocking Yugi. He hadn't thought what Yami did was that bad compared to the past. He tries to reassure Tea but she still won't relax around Yami.
Ryou senses the Shadow Realm growing stronger and begins to worry. Bakura heard about the museum trip from Ryou, and is furious that the pharaoh doesn't have any memories so his revenge would have no meaning. Ryou tries to distract Bakura from it, but Zorc manages to speak to Bakura and encourages his rage, not letting Bakura listen to Ryou. Seto finished setting up his tournament and sent out invites to all the players. Malik entered the tournament with Odion pretending to be him, as the group was told by Isis that her brother is here and planning on destroying them. Malik's unaware that Odion only is doing this to keep Marik bound where he can't do anything.
Before the tournament can officially begin an idiotic rare hunter from Malik's group steals Joey's Red Eyes. Joey falls into a depression. He couldn't protect his sister who needs eye surgery, having to accept money from Yugi to pay for it, and he couldn't even take care of the card he'd formed such a strong bond with despite all he'd done to get stronger. He disappears just before his sister's due for surgery, and she's too scared to take it without him there. Yami and Yugi work together to track down Red Eyes to help Joey, desperate to get him there to help his sister. They pull a shadow game on the rare hunter. Malik realizes the rare hunter is acting up when he picks up the Shadow Magic and checks on it through the hunter. Furious he withdraws his help from the hunter, simply watching to learn more about how the pharaoh and his host duel. The Red Eyes is rescued, and is used to get Joey to the hospital in time. The hospital is shocked to see a dragon, but passes it off as a hologram, and Joey's sister gets the surgery she needs. Now ready for the tournament they prepare, knowing it'll be the center of the shadow games.
Bakura and Ryou don't enter the tournament this time, as Bakura is distracted by the fact that the Necklace and Rod are now within reach and is busy trying to locate them. Ryou is careful to keep Bakura from knowledge about the tournament not wanting to enter in another one. It's obvious as the tournament goes on that Joey's magic is getting stronger, more and more of his games done with shadow magic.
Yami and Yugi end up dragged into a shadow game with someone claiming to be the rightful holder of Dark Magician. Furious to see a false Dark Magician the real Dark Magician materializes and attacks. Yami and Yugi have to be careful in their actions though, the 'magician's lair' is full of traps. Yugi's Light magic ends up revealing the truth of the tricks, with Yami's Dark magic keeping their own side hidden, and together they manage to defeat the opponent. Glad to have it confirmed again that Dark Magician is theirs, no one else's, Dark Magician and Yami head to the Shadow Realm to celebrate. In the celebration Dark Magician accidentally lets slip he knows Yami's past. Yami assures Dark Magician it's alright, that he doesn't want to know the past, that he's no longer what he was.
Malik gets impatient, and gives one of his puppets Slifer to challenge Yugi, staying close so he can use his full magic this time. He's frustrated to find that Yugi and Yami are working together as well so they can't get the advantage. Malik and Marik still manage to push them however and chances are they'll win. Subconsciously Yami reaches for help. Seto feels something pull him to the deck, and is shocked to find Yugi losing. Angry that HIS rival and equal might lose to someone else he snaps out a clue that lets Yami win. The penalty game unleashed backlashes on Malik due to how close he is and knocks him out. Odion helps stop Marik from coming out with Malik unconscious, Marik growing angry that he's not allowed out despite the fact that again someone has hurt his host. He's losing his mind being trapped as he is. Yami claims Slifer from the game, the god spirit deeming him as worthy so he can use the card without danger. Marik tries to force himself out despite the barrier, the pain of the desperation to escape driving Malik to wander away from the others. The surge in shadow magic from the struggle finally allows Bakura to locate Malik.
He reveals that he holds the Ring, and Marik snaps that it doesn't matter. Malik follows Marik's lead asking why he should care. Bakura recognizes that Malik's too unstable to see the bigger game and takes advantage of it, pretending to want to help them. Marik warns Malik not to trust a Dark, but Malik ignores him and asks what kind of partnership Bakura would be interested in. They work out that Bakura will help Malik get the cards and in exchange he will be given the Rod. First they'll have Malik get closer to Yugi's group by pretending to be one of their friends. Ryou tries to protest, but Bakura soothes the gentle soul and submerges him so he's asleep before stabbing himself in the arm. As soon as they find the group Ryou lets Ryou out, telling him to go along with Malik being someone called 'Namu', as it's a way to get an item without killing the holder. Ryou goes along with it, not wanting anyone else to die. As soon as they're set up in the hospital Bakura takes the pain of the arm onto himself, using shadow magic to restrict Ryou's movement so it can heal since Ryou himself wouldn't be able to feel the limits.
In the hospital Bakura learns about the tournament, and he's furious that he could have used it to get what he wanted without a partner. Ryou apologizes. Bakura grumbled about it but he's resigned to his current route. Not much else he can do. Malik as Namu learns Tea, Joey, and Mokuba are Seto and Yugi's weaknesses, a perfect chance to destroy the priest's reincarnation and the pharaoh at the same time. He kidnaps them, and as Namu lures Seto and Yugi into a duel. They win, only to find that Tea and Joey are being mind controlled. Mokuba is safe, but Tea is holding a cyanide pill in her mouth, ready to swallow it if Yugi refuses to duel against Joey in a deadly game. Yugi has to duel without Yami. It turns into a shadow game. When Red Eyes comes on the field Joey partially wakens through the bond formed between them, but it's still not enough. The Puzzle has to do the rest of the work. They manage to break the control of the Rod to Malik's frustration and both end up safe.
Bakura recovers enough to leave the hospital as long as he remains in control of the body and talks with Malik again. They agree they need to work closer together so Bakura uses a shadow game to take the place of a tournament player. With the first half of the tournament over the finalists board a blimp. Yugi's shocked to find that his first duel is against who he thinks is Ryou. He finds it's Bakura, and Yami and Bakura go head to head with Slifer pulled out. Malik tries to tell Bakura how to duel and they end up fighting. When Slifer's set up to attack and finish the duel Malik uses the rod to force Ryou out, believing that Yami wouldn't attack one of Yugi's friends. Ryou's confused about what happened, and in pain with Bakura shoved out of control, not able to hold back the pain in the arm. Freaking out Bakura acts to protect Ryou, but since it's a shadow game it has real consequences. Both him and Ryou are drained, knocking them unconscious without enough strength to do anything further. Malik's furious to lose his partner, and sets Odion as the fake 'Malik' into the next duel. Joey's excited at the chance to take 'Malik' out as payback for what was done to him and quickly turns it into a shadow game determined to wipe out the threat. Malik slipped a fake Ra card into Odion's deck, telling him to use it to convince them that he really is Malik. Odion begs not to do so fearing the consequence of angering the god spirit, but Malik simply threatens to control him to do so if he won't. Odion reluctantly summons the fake Ra, angering the real god spirit. Ra turns on Odion and attacks him. The man's badly damaged, thankfully kept an inch away from death. With Odion's fall the group realizes he couldn't have been the real Malik, or Ra would have responded for him.
Odion's fall breaks the barriers keeping Marik locked away. Seeing his brother collapse Malik panics realizing that he's gone too far and needs to stop. Marik, having gone insane from being trapped and unable to do anything, freaks out and takes over the body forcing Malik out. He will not let anyone get in their way, not even Malik himself. Marik will destroy everything that tries to stop him. Laughing maniacally he reveals who he is. Malik desperately tries to return to the body, but Marik refuses. It's his first time being allowed out in five years since he killed Malik's father, he deserves time in the body. He snaps that he'll destroy Malik if he insists on trying to get in his way.
Finally in control Marik has his first duel against Mai, also a finalist in this game. Mai refuses any help against the insane Dark and ends up having her mind shattered so she's trapped with no memories in darkness, unable to get back to her body. The group tries to convince Seto to take them to a hospital to fix Odion and Mai, but Seto insists the onboard doctor can take care of it. The group's panicking, but Seto still refuses to acknowledge the existence of magic, and continues the tournament as if nothing's wrong, set to compete himself against Isis next.
Isis' Necklace gives her a vision that Seto will lose the duel by using Obelisk. She taunts him that way, Seto relying heavily on the card as it's the most powerful in his deck and he relies on power over everything else. He is about to lose when he draws Blue Eyes. The connection between them sends a flash of Blue Eyes from the past when he was a priest. It's impulsive, but he decides to trust it and rely on Blue Eyes as he always did in the past. Breaking the vision he wins instead of Isis as she predicted. Shocked at her loss Isis feels she was too proud and reliant on the Necklace. She thinks her time as a holder is over, and gives the Necklace over to Yami and Yugi for safe keeping, her role in the larger game finished. Now all she can do is hope her family will come back.
Malik finds himself trapped in the Shadow Realm. He manages to fight his way through it to contact Bakura and ask for help. Bakura's furious when he learns that the Necklace was lost to the pharaoh and his host, leaving them tied. He demands to immediately be given the Rod and Ra in exchange for his help this time. He is furious on how Marik was treated, spitting at Malik that it's only this way because he didn't let Marik do what he'd been made to do, upset that if he had been a young spirit like Marik Ryou could have abused him the same way. Bakura manages to siphon enough energy from Ryou to challenge Marik to a duel. Unfortunately the entire time Malik and Bakura argue. When Marik summons Ra he defeats Bakura, sending their body to the Shadow Realm. Bakura and Ryou split in the Shadow Realm, Bakura furious that Ryou ended up endangered by Malik's reckless plan. Ryou asked Bakura what was going on, and Bakura explains, hiding that he's connected to the Puzzle and might be able to use it to get out. Malik, Ryou, and Bakura form a temporary alliance to survive in the Shadow Realm.