When Bakura lost to Marik, his body was banished to the Shadow Realm, Malik thrown in after him to prevent any further attempts to regain his body. In the Shadow Realm Ryou and Bakura separated, each having their own bodies in this realm. Bakura was furious to realize that with the body in the realm with them they were separate, leaving Ryou endangered. Ryou asked what had happened, Bakura roughly explaining that he had lost a battle that had lead to them being trapped here. Zorc convinces Bakura to keep his connection to the Puzzle a secret, as only one could use it as an exit.
Malik Ryou and Bakura enter a temporary alliance to survive here, Bakura having no choice but to rely on Malik to help his host. Bakura teaches them how to survive here and function, with Malik explaining that him and Ryou are Light, and teaching Ryou how his magic functions as Bakura cannot. Malik reveals he might have a way to contact those on earth still, so Bakura and Ryou make base and protect it while Malik contacts his sister and explains that the three of them are trapped in the Shadow Realm. Isis agrees to use her magic to once a day create a point of contact that would let them come back to the blimp instead of anywhere else the Shadow Realm might spit them out when they find a portal to go back. Unfortunately that's all she can do on the outside, it's up to them to get themselves out as long as Marik is undefeated.
As they fight the shadows Malik is impressed to see how adept Ryou is in his magic and surviving. Bakura doesn't explain that he'd actually been training Ryou from the time he realized he could one day use Ryou to be the perfect host, training him in fighting and what magic he could with the differences in their natures. Bakura ends up as the unofficial guide in the group. His protective side is quite obvious here, as he can't hide Ryou away or do what he normally does to make sure Ryou isn't pulled in. Ryou's glad to finally have solid proof that he was right about Bakura caring for him.
Malik complains about Marik and how he's so different, abusive and violent instead of acting as the other Darks do with their hosts. Bakura snaps at Malik, revealing his fear that Ryou would have left him trapped how Marik was if he could. Malik realizes that Marik's crazy because of what he did. It's his fault his Dark is so crazy. He decides to try and help in the future.
The shadows try to lure Malik from the group, as Bakura and Ryou are balanced together, but Malik's vulnerable. Bakura and Ryou realize they need to act together to cover the other's weaknesses, Bakura forgetting the contract with Zorc that protects him from most of the dangers of the realm, and combine their powers to protect Malik. Unfortunately the constant battle is slowly draining the group. They need a Dark for Malik or they'll eventually all die.
On earth Joey, Yami, Yugi, Seto, and Marik are preparing for the final shadow games. They're the last four in the tournament. Seto's still in denial of the magic, leaving Joey, Yugi, and Yami to strategize together to try and stop Marik, knowing he'll be unstoppable if he gets all three god cards like he wishes. In the midst of this planning the blimp is suddenly hijacked by a hack into the computer navigator. They're pulled off course, and learn that an AI is planning on killing all of them-unless they're willing to put their bodies on the line and play a game against him. Tea, Tristan, Joey, Yugi, Seto, and Mokuba all volunteer to place themselves into this contest. Marik refuses despite the danger this could lead to. Isis agrees to stay behind, and make sure those who are unconscious can't be harmed by Marik while they deal with this problem.
They enter the virtual game and learn that it's based on Seto's past and exploiting the weaknesses there. In the real world Marik contemplates destroying the bodies while they're lying there. If they die, nothing can stop him from simply taking the cards. Isis however invokes her own game, dragging it out so Marik doesn't have the chance to attack. In the game Yami and Yugi separate. They find that forcing Yami's presence into the game again creates a split, allowing the Shadow Realm to merge into the game.
Ryou, Bakura, and Malik sense the disturbance where they are in the Shadow Realm and head over to investigate it. They're relieved to find that again they have a chance to interact with those still on earth, only to be disappointed to learn that no one they want to contact is here. Ryou doesn't trust them either after the time spent growing tougher in the Shadow Realm. After all, he's faced Yugi's group before, and unless they're fighting Bakura he's just on the edge. They didn't help him out with reality the way Bakura did. They'll have to stay hidden. Malik is initially excited to learn it's a battle for bodies, but is quickly frustrated to learn that Marik avoided it entirely. He won't be able to get his body back this way. They keep to the edges of the game, helping the group out where they can.
As the game continues Seto's past in the orphanage and abuse is revealed. Bakura cracks up laughing over it, knowing the truth of who Seto once was. Yugi's group eventually finds Noah, the AI that trapped them. They learn that he was Gozaburo Kaiba's real son, turned into an AI after a car accident that destroyed his body. He's jealous of Seto taking his place, and wants his place back. The group fights beside Seto to escape from Noah, only to discover that Gozaburo is the real mastermind, not dead, but hiding as an AI himself in the computer.
Noah's quickly abandoned for 'failing' in getting any of the bodies from the group. They turn to fight Seto's 'father', and Noah changes sides freeing them from the machines. As thanks Yami alters Noah, using the meshing of the Shadow Realm and the virtual world to alter Noah so he is now a shadow spirit, and able to live a life in the Shadow Realm rather than bound to a virtual world that's too predictable. Bakura, Ryou, and Malik are ejected back into the Shadow Realm with Noah as the virtual world is completely destroyed, removing any chances of Seto's father coming back again.
Bakura's group meets up with Noah, and use the new shadow spirit to temporarily balance Malik. They explain to him how the Shadow Realm works. The trio uses their magic to anchor Noah's human memories so he can survive without being torn apart by the shadows. Here he gains a fighter form, no longer human in appearance. Noah doesn't really feel bad about it, as he wasn't really a human for years. His new form is that of a raiju. He can shift to a humanoid form to talk to them still, but clearly prefers his new form and loves his new home.
Yugi's group managed to exit the machines just as Marik wins against Isis and starts destroying the pods that had held them in the virtual world. Marik is annoyed, but announces that they'll finish this in the tournament.