When Bakura and Ryou return from the Shadow Realm everyone's shocked to find them partially separated. Ryou is as he always was, but Bakura actually can interact with physical items soaked in shadow magic, and is visible and audible to almost everyone. With most of the blimp drenched in magic it's like he has a body of his own. Malik realizes he separated them by accident, as he's used to seeing them as two separate beings. Bakura quickly experiments with the limitations, and learns he can only go 100 feet away before he's stopped. He's still a spirit and bound to Ryou.
Malik feels better now that Marik is resting and no longer filling his head with anger and hate. He knows he has a lot of work to do with his Dark, but at least he has a starting point. He leaves Isis and Odion. The pair's told it's for the best. They're reluctant to leave but do so, as Isis now needs Odion more than Malik does and Isis fears Malik still from Marik's possession.
Yugi is excited about Bakura having a separate form from Ryou, even if Bakura scares him, and mimics Malik, resulting in Yami getting a partial form as well. He uses this to start teaching Yami how to be human and interact with the modern world, something Yami had struggled with when possessing Yugi. They learn the spirits can still possess their hosts and go back into their Items, but for the most part they're happy for the new freedom this partial form gives them.
It doesn't take long to notice that there's an increasing number of shadow games happening with people who don't have Items. More and more people are using magic. They realize the seal's becoming rapidly undone.
The Kul Elna spirits return to Bakura's side as the seal weakens, again whispering for revenge and clouding his mind. When a poker game at school using duel monsters accidentally becomes a shadow game the school panics, leading to it temporarily shutting down.
Seto decides to begin tracking the progress and possibilities of shadow magic so he can figure out what to do as it will affect his company in a major way. He makes a website with Mokuba to do so.
Bakura acknowledges the spirits, and begins to again obsess over collecting the rest of the items, even attacking Yami. Ryou learns who the spirits are and struggles calming Bakura down as the effect of the spirits are gaining strength on the ancient spirit.
Seto begins posting what he learns on the website, and it begins to become extremely popular. He has to start a subunit of the company to keep up with his Shadow Realm research.
Malik contacts the wounded Marik to begin helping him heal. He finds that Marik's terrified he's been trapped again. He decides to give Marik a chance to be in control, but Marik is still too unstable and ends up hurting lots of people. He brings him back in, and realizes he'll need someone to help supervise Marik as he won't be in control of the body when Marik's out. He recruits Bakura and Ryou to help. It's difficult, as Bakura is having increasing trouble focusing on things outside his revenge, but when they get Marik to start calming down they discover that the mad spirit is extremely childlike beneath it all, still very young and curious about the world.
When Bakura loses control and lashes out at Yami, the pharaoh spirit reveals he doesn't want to be tied to his past and wishes for people to stop looking at him to fix it. He's just Yugi's protector now.
With Bakura losing control Zorc pushes as Bakura weakens, and pulls Shadi to them. Shadi is challenged to a shadow game, and loses to Zorc/Bakura. Zorc/Bakura turns to attack the others. Scared at Bakura's sudden change Ryou barely manages to get a warning out to the others before he's trapped. The group realizes this must have been why the Shadow Realm was sealed before, and that Bakura's been tied to the demon. They look up spells to seal a demon away, but there aren't many. The god spirits help, but find that the spirits of Kul Elna are blocking them.
Ryou finishes putting together the clues about Bakura's past he's found over the years and explains it. He offers himself to the spirits to try and pacify him. The spirits are drawn to his Light, and Malik, Isis, and Odion work together to use a ritual to allow the spirits to find peace. They find their ritual is actually destroying the Items as it goes on. The Lights panic as the Items work as anchors for their Darks, the Darks growing worried that they'll be banished again and torn apart by the shadows without anything to stop it this time or any chance of escaping. Seto reveals he'd found a way to make replicate vessels in his research, and manage to safely transfer the Darks over just before their Items are destroyed.
Moved over the Darks are again just spirits without the partial forms of before. Zorc is still loose however, but currently unable to come through. The group retires to recover. They try to convince Ryou to let Bakura go as Zorc is tied to him, making him extremely dangerous. Bakura realizes he can no longer sense the spirits of his family and goes crazy calling for them. Ryou comforts Bakura and protects him from the others, refusing to let them sacrifice him.
Zorc is furious and decides to use Bakura as his vessel, and reveals a spell to give a physical body to the group, hoping they'll use it so he can jump into Bakura. The group dissects the spell to make sure it's safe. They find the trap, but manage to actually use it to find the original binding to Bakura and undo it. They finally manage to seal Zorc, and the spell Zorc 'gifted' them is used to give the Darks bodies of their own.
The bodies aren't entirely human, as the Darks are no longer human, the group altered with the heavy use of magic halting the aging of everyone but Mokuba, who will most likely stop aging when he reaches their age. The group discusses what to do next, and decide to disappear as they're far too famous, and don't want to have to deal with the problems of the Shadow Realm returning.
Seto becomes an expert on shadow magic and sets someone up to pretend to be him so he can leave with Mokuba and live a quiet life while still pulling the strings. It doesn't take long for them to realize that the Darks can't separate from their Lights, as attempts to do so tend to bring immediate deadly consequences targeting the weaknesses existing from not being properly balanced. They set up their lives, Ryou and Bakura together, Ryou trying to help the grieving and abused tomb robber adjust to a new reality and try and keep him from getting caught as he's still a thief, Malik and Marik enjoying the modern world without limits and Malik teaching Marik how to trust and not destroy things, and Yami and Yugi happily delving into shadow games and finding new challenges to face, Yami still the protector and still unwilling to ever take charge again. When they can the group meets up in the Shadow Realm, Seto having kept the secret of how to travel there from the rest of the world so it remains a private place for them to meet up when they wish. Seto only reveals what's necessary to the world so the Shadow Realm remains safe.
With magic back in the world things begin to change. Pollution is solved. Resources are not a problem. Magic replaces technology in a lot of ways.
And so the world returns to the balance it was meant to have.