The Ishtars had been assigned the task of protecting the pharaoh's name in case it would be needed to renew the seal against Zorc. Despite the new lack of magic rituals were followed for when magic would return to allow them to keep the name hidden and only have it revealed to the pharaoh himself. Unfortunately thousands of years separated and hidden from the world corrupted the clan. The original rituals changed with time, and it became more of a cult than the tomb keeper clan it was meant to be, forbidden to interact with the outside world. They remained underground, living the same way as they had when the pharaoh had been alive.
The head of the Ishtar family loved his wife, but when she bore a girl, Isis, he was disappointed. He was told by their healer that chances were she could not have another child. He was disappointed, but as luck would have it the son of a thief had managed to stumble to their hidden door. He was adopted as only male heirs could carry on the secret of the pharaoh's name. His name was Odion.
Three years later it turned out that the healer had been wrong. His wife gave birth to a boy, and Odion lost his place as the heir. Still, he had been rescued from a terrible life, and he didn't begrudge the young boy that took his place. He might no longer be considered family by his adoptive father, but his brother and sister needed him as their mother had died giving birth to Malik. He protected them from their father's abuse, and dutifully memorized scriptures alongside them.
Malik was more shielded than Isis and Odion. They knew the horrors that would come to him when he was old enough and so did their best to keep the harshness of their world hidden and spoil him. He was insatiably curious and wanted to see the world outside. Shadi, the guardian of the Items, had found the Ishtars and believed they would be worthy holders of the Items. When he discovered the tomb keepers were now little more than a cult he was disappointed, and gave Isis the Millennium Necklace and Malik the Millennium Rod in the hopes it would help them. When Malik was ten it was time for him to undertake the ritual and have the secrets of the pharaoh's name carved into his back.
The ritual was corrupted, and painful as each marking was etched with care deep enough to ensure that it would scar. The ten year old begged for something to make the pain stop, for his sister or brother to rescue him. When they didn't come to stop the ritual he begged for something, anything else to help him. The corrupted ritual combined with the Rod granted his wish. His Dark half was torn from him, leaving him unstable and worse than before as he had never been particularly Light in the first place, and was used to create a Dark guardian for the boy.
The spirit was young, and nestled deep inside Malik's mind. It took the worst of the pain of the ritual if not the entire memory, and consumed Malik's hate, fear, pain, and rage. That was it's world. Odion sensed something had happened with the ritual, and took desperate steps to protect his brother, carving his face with symbols to permanently protect and follow Malik. The symbols kept the Dark spirit from being able to emerge and grow, trapping it in the Rod. It had been created for one purpose though, and it was not one that it would let go.
Malik was unaware of the change as the Dark spirit's attachment to him prevented the negative consequences that normally come with splitting oneself into Light and Dark. Isis received a vision from her Necklace shortly after, and spoke to Odion in terror of what it meant about Malik. Odion promised to keep an even closer eye on the sibling from now on. Odion's presence kept the spirit weak and from emerging for a year, though it could whisper to Malik, angry about the pain Malik experienced and hoping to escape. Malik took a long time healing. He dreamed of the world outside of the tomb the entire time. When his next birthday came he convinced his sister to take him outside. For one hour they would explore the world beyond the underground catacombs they lived in while Odion provided a distraction.
He fell in love with that brief glimpse of the outer world and never wanted to leave it. Shadi sensed the shift as Malik made his choice. He found the Ishtars and tried to warn them to hurry home, but they were too late. They'd been discovered missing by their father. They returned to find him beating Odion to death. Odion passed out, the barriers trapping the Dark spirit falling. When the father turned on them the Dark spirit gained enough power from Malik's guilt, terror, and pain to take over the body. The Dark spirit pushed the father away and pinned him to the wall to punish him. The spirit's furious when Isis tries to interfere and strikes her, using shadows to bind her. The spirit plans on punishing her for helping Malik's enemy after the father is dealt with.
Isis continues to call for Malik, giving the spirit an idea for an identity. He names himself Marik, the young spirit finally old enough to have some semblance of self. He introduces himself, making it clear that Malik is currently not available. Marik tortures Malik's father to death. He would have moved on and punished Isis but he was still too young and weak to stay out for so long. He falters, and Odion wakes up. Odion recognizes that Malik is possessed and tries to call Malik back. Marik is too weak, collapsing, and finally lets go deciding Malik is safe for now.
Malik doesn't remember what happened, and is terrified to find his father dead, if relieved at the same time. The siblings don't tell Malik what happened, the trio forced to flee fearing the cult's reaction to their leader's death. The group struggled to survive in a modern world they knew little about. Malik adapted perhaps too rapidly, Isis worried, and growing scared at Malik's lack of morals. Marik is too weak to come out around Odion, and is still very young and needs to learn more. Odion uses that to trap the spirit so he can't come out again, leaving the spirit with nothing but the negative emotions that created him and the knowledge that he exists to protect Malik from all that would stand between him and his host's happiness. He works to keep Malik happy, whispering encouragement when he can, and soothing the hurt when Malik doesn't follow the law, convincing Malik that he's right in what he's doing.
Isis adapts and finds work at a museum, but under Marik's influence Malik grows wilder and wilder. Marik encourages the freedom, but starts to grow angry as he realizes that Odion knows he's there and is actively blocking him, keeping him from protecting Malik. He feels that Odion is in their way and tries to convince Malik to leave Odion. Malik starts a gang of bounty hunters that collect rare items, focused around duel monsters. He grew up hearing of the God cards and how they can be used to shape the world, and thinks that if he could get them all he could finally escape the nightmares of his past and live happily. Odion knows it's wrong, but he's too loyal to Malik to leave him despite it.
Malik decides he wants revenge on the pharaoh who was the reason why he had to live underground and will destroy everything that had to do with him. Isis is terrified to learn of Malik's plan and tries to stop him. Marik almost breaks out to hurt Isis for trying to hurt Malik but Odion interferes, leading to Odion and Malik fleeing Egypt and leaving their sister behind. When Pegasus uses his Eye to find Item holders Isis and Malik both receive an invitation. Isis of course refuses, knowing there's no chance that Pegasus can actually get in touch and harm Odion or Malik. Malik, under Marik's influence, creates a mind puppet to enter the tournament for him to find out more about the other Item holders and see if there's anything useful there. His puppet doesn't stay long. When the tournament's over he hears of a new tournament being formed, and knows his sister went to the holder of it. He knows Isis is planning something, but isn't sure what. Still, it seems time to make his move as he has managed to get two of the God cards, Slifer the Sky Dragon and the Winged Dragon of Ra. It's time for his revenge to begin.