Narrowly escaping Marik killing them in the virtual reality pods the tournament quickly resumes. They reach where they were supposed to go and a four way duel is set up to decide final pairings. Yugi is afraid of what will happen if Joey is paired against Marik so ends up sacrificing points he doesn't have to to try and protect Joey. Joey's furious, and says he can hold his own. He convinces Yugi to let him fight alone and he proves his strength when he takes Marik out of the duel. Unfortunately he's next, pairing him with Malik and Seto with Yugi.
Marik and Joey duel in a shadow game where they're shocked whenever they lose life points. Trying to keep up with Marik Joey overextends his magic and faints before he can win. Marik tries to punish Joey, but the shadow game declares Joey's punishment already spent and won't let Marik harm him. Yugi's worried but the Necklace gives him a vision that Joey will be alright, giving him the courage to keep going. He duels with Seto next. Seto combines his virtual technology with shadow magic, making him much more confidant and able to keep up with Yami. The price for the game is each other's god cards. It's a close duel, far too equally matched and the gods destroy each other. A part of their past is shown in the explosion of a similar duel, and they choose to again rely on those they've always trusted, Dark Magician and Blue Eyes White Dragon.
Yami wins and receives Obelisk. Joey wakes up. The group celebrates that he's okay, Seto struggling with accepting magic and his loss and snaps at Joey. A harsh shadow game between Joey and Seto begins to prove magic, Seto winning once he accepts that Blue Eyes is in fact real. Torn by this truth he struggles to reconcile his knowledge of his past life with who he is now. Mokuba helps, pointing out that the past doesn't dictate the future, and that Seto CHOSE to come twice.
Seto accepts that, feeling more in control, and wonders what he'd planned for him to choose to come back. Yami finally faces Marik in a shadow game. Malik is suddenly pulled from the Shadow Realm to be a pawn for Marik, the constant battle in the Shadow Realm leaving him too drained to fight the pull. Bakura, Ryou, and Noah work on trying to bust Malik out from inside the Shadow Realm. Yami's shocked to find Yugi's been pulled out as well, the Light souls placed on the line for the shadow game. He determines to win even if it kills Malik to save Yugi.
The duel is incredibly painful, the Lights slowly being torn apart with Yami desperately trying to stop it. Bakura remembers Odion, and tells Ryou to wake him up. Odion is dragged awake by a full blast of Light magic. Realizing something's going on Odion hurries down to try and suppress Marik. Bakura realizes he can't help anchor someone the way he had been and lets go. Ryou retires with Bakura back to the Shadow Realm with Noah and watches the duel continue.
Marik is weakened by Odion's presence, and gets scared. He uses Malik to fuel Ra into his ultimate form to destroy Yami. Malik finally understands what Bakura was saying about Marik and reaches for him. He promises to take care of him and not hurt him again. He manages to switch places so he's now the one dueling and Marik's the one on the line. He alters the game so Marik won't be destroyed, only banished to the Shadow Realm. The game finishes with Yami winning thanks to Malik and Marik sent to the Shadow Realm. Bakura cheerfully greets Marik, and proceeds to beat him up.
Malik gives Yugi Ra so he now holds all three god cards, and shows him his back revealing the secret of where Yami's name is hidden and the secret of his past. Yami thanks him, but he's not interested in his past or his real name, content with his current life. Malik works on undoing Marik's magic, bringing Mai back and the others hurt, and brings Bakura and Ryou back. Marik is also brought back, tied to the Millennium Rod so they're now separate, and gives Marik a safe place from the shadows.