Marik's family guarded the tomb of the Pharaoh for generations and two Millennium Items (the Millennium Rod and Millennium Necklace) were passed on to Marik and his sister Ishizu Ishtar. Marik was forbidden to leave the Pharaoh's tomb due to his father's fear that the freedom and marvels of the outside world would further divert Marik's attention from his heritage. Marik no longer wanted to become a Tombkeeper, so his adoptive brother Odion Ishtar asked if he could take Marik's place but Marik's father rejected the thought of Odion taking Marik's place. When Marik was forced to take the initiation ritual to become a full Tombkeeper, Marik spawned his second personality Yami Marik from the pain he endured. A year later, Marik and Ishizu took a forbidden trip to the surface but their father found out and attempted punish Odion, for not stopping Marik and Ishizu, by killing him. In the midst of his father's torturing Odion, Marik blanked out and his second personality Yami Marik emerged for the first time to resist his father's punishment and stole the Millennium Rod for himself. Ignoring his father's orders to put it down, Yami Marik used its powers to hold him against the wall. When Ishizu protested, she suffered the same strike. Yami Marik then proceeded to kill his father with the Rod's short blade (this part was cut out from the dub). After Yami Marik was sealed away in Marik's body by Odion, Marik believed that the Pharaoh had ordered the loyalist Shadi to kill his father, due to Odion saying Shadi had killed him, trying to be a big brother and hiding from Marik that it was actually his alter ego who had done so. This increased Marik's grudge and resentment to the Pharaoh, causing him to leave and start the Rare Hunters.

As a teenager, Marik was the leader of the Rare Hunters organization and he uses the Millennium Rod to obtain the three Egyptian God Cards so that he could take their powers, gain the title of "Pharaoh" and set his family free from the duty of the Tombkeepers (In the dub, he wants the Pharaoh's power for himself and use it to rule the world). He also has a second agenda, to get revenge on the Nameless Pharaoh's soul for killing his father as he mistakenly believed that it was the Pharaoh's fault. Although he and his Rare Hunters uncovered "The Winged Dragon of Ra" and "Slifer the Sky Dragon" from where Maximillion Pegasus had hidden them, they were unable to get "Obelisk the Tormentor", which was taken by Ishizu and given to Seto Kaiba.