|“||I'm the true Marik, and I'm not as kind as the one you've come to know.||„|
|~ Yami Marik|
The spirit of the Millenium Rod, DarkNite was the creator of the Shadow Realms and a god-like being with the power to turn Mortals into cards.
DarkNite is sealed in the Forbidden Temple but is eventually unsealed by Heishin, who he then kills.
Atem and Seto then proceed to duel DarkNite, Atem defeats him in both his normal and Nitemare forms and he is sealed away again.
Yami Marik was awakened out of Marik's hatred and anger at the Pharaoh for having to be his tombkeeper, along with Nitemare's spirit in the Millenium Rod. He took over Marik's body and imprisoned his father in the Shadow Realm, but was contained by Odion. Yami Marik did murder his father in the Japanese version (he sent his father to the shadow realm in the dubbed version), he almost did the same thing to Ishizu, but was stopped by Odion.
When Odion was knocked out by the Winged Dragon of Ra, Yami Marik was able to reawaken within Marik, possessing his body and trapping him inside his mind. He proceeded to duel as Marik Ishtar in the tournament.
Yami Marik's duels were all twisted shadow duels. In the quarterfinals, he dueled Mai Valentine in the Shadow Realm, in which whenever a duelist lost a monster (to an attack by their enemy), someone would be erased from their memories. Unlike Mai, Yami Marik did not mind this at all, as there was no one in his mind worth remembering. He lost Strings and Arkana during the duel. Mai managed to steal and summon the Winged Dragon of Ra, the most powerful of the three God Cards, but was unable to control it, so she was defeated trapped in the Shadow Realm. In the manga, the duel is even more creepy and disturbing as each contestant felt the pain caused by their loss of monsters and direct attacks as if they were real, along with illusions of blood and decapitation, and Mai was trapped in her own mind, where she would ultimately die if Yami Marik was not defeated within 24 hours.
Later this night, Yami Bakura dueled Yami Marik on the request of Marik's spirit who wanted to to regain his body. The two evil spirits dueled in the Shadow Realm, in which whenever a player lost life points, their body would vanish. Yami Marik won and Yami Bakura was trapped in the Shadow Realm (though he escaped to Yugi's Millennium Puzzle). In the manga, Yami Bakura was temporarily destroyed, though the part of him inside the Millenium Puzzle allowed him to remain.
Enter the Shadow Realm
The tournament was interrupted when Noah Kaiba made the blimp land at a station where his virtual world was located in. After Noah set the virtual world to explode, Yami Marik destroyed the control center so it could not be stopped.
Battle City continued from here, and a four-way duel between Yugi, Kaiba, Joey, and Yami Marik was held to decide who would face each other in the semifinals. Yami Marik and Joey both lost (as Joey intended), so they dueled in the semifinals. Yami Marik took their duel to the Shadow Realm, in which players would lose life energy as their monsters were destroyed. (In the manga the contestant once again felt the pain of their monsters, just like anytim Yami Marik launches a Shadow Game.) Joey held his own against Marik and resisted to the Dragon of Ra's attack which should have reduced him to dust. Just as he was about to win, he collapsed from the energy he lost, and Yami Marik won by default. However, Joey's soul did not go to the Shadow Realm/Joey survived and only fell into a coma.
Yami Marik dueled Yami Yugi in the final round, in which both Marik and Yugi, their original selves, would disappear whenever they lost life points. (Either to be destroyed or trapped in the Shadow Realm, following the manga or the anime.) Eventually, Yami Marik's Winged Dragon of Ra was destroyed, and Marik and Yami Marik were switched around, making Yami Marik the victim. No longer evil, Marik decided to forfeit the match so the Pharaoh could fulfill his destiny. Yami Marik tried to convince him not to, but was unsuccessful, and as Marik lost the duel, Yami Marik was destroyed, and Mai released from the Shadow Realm.
Waking the Dragons
An apparition of Yami Marik appeared as a lost soul alongside Bandit Keith, Arkana, Seeker, the Paradox Brothers and Panik; as Yami was trying to get to Yugi, whose soul was taken by the Orichalcos. It is unlikely that this was really him (as opposed to some sort of illusion), however, as neither Arkana, the Paradox Brothers, nor Bandit Keith were dead, in the Shadow Realm, or taken by the Orichalcos. It is possible, however, that they were all sent to the Shaw Realm after failing their former masters (or in Yami Marik' case servants) a Millenium Item, and thus had the power to banish souls to the Shadow Realm.