The Millennium Items appear in various fan-fictions.
Yu-Gi-Oh! X - When the curator of the Domino City Museum defiles Pharaoh Seto's tomb and unleashes an ancient evil, Shadi uses the curator's soul to recharge the Millennium Items for the coming dangers. Shadi remained in possesion of the Millennium Key and the Millennium Scales. He then held several tests to check the worth of Yugi and Kaiba's sons, Tag and Seth, in receiving the Millennium Items along with their friend, Darin. Tag gains the Millennium Puzzle. Seth gains the Millennium Rod, and Darin gains the Millennium Ring. The three then use them to help defend their family and friends for several weeks aftwerwards. Shadi also returned the Millennium Eye to Pegasus to allow Pegasus to make a new set of Egyptian God Cards. After Tag won the tournament Pegasus made to give away the cards, Anzu gained the Millennium Necklace.
The Little Dark Magician Girl - The Millennium Items are used by Prince Atem's court, but Atem doesn't complete the Puzzle until the story's almost over, and they're the only defense against the mind-controlling power of Vivian's Millennium Stone. Atem ends up with the Millennium Puzzle, Seto has the Millennium Rod, Aknadin has the Millennium Eye, Isis has the Millennium Necklace, and Mahad gets the Millennium Ring after he becomes a permanent human.
The Little Dark Magician Girl II: Return to the Ka World - The Millennium Items are still being used by the people who had them at the end of the first story.
Kisara and the Beast - Ishizu uses the Millennium Necklace to see Kaiba and Kisara confess their love for each other.
Yugi Moto - The puzzle box that Anubis was after was turned over to Yugi's possession since he, Joey, and Tristan got stuck in the cave. In boredom, Yugi began to solve the pieces and unleased the power of the Millennium Puzzle, which held Yami trapped. In the end, Anubis gets trapped in the Pyramid of Light and Yami is no longer trapped inside the Puzzle.
The Return of Anubis - Yami still has the Puzzle, yet he's not held back by it.
The Egypt King - At the beginning of the story, Aknamkanon has the Millennium Puzzle, Seto has the Millennium Rod, Aknadin is the bearer of the Millennium Eye, and Shadi has the Millennium Key. When Aknamkanon is killed, Atem takes the shattered Millennium Puzzle with him into exile as a way to keep his father with him. Seven years after Aknamkanon's death, Mahad gained the Millennium Ring, beating out Bakura, and the following year, he was killed, and Mana gained the Ring next. Atem eventually completed the Millennium Puzzle after eight years and became its bearer.
Yu-Gi-Oh! Beauty and the Beast - Ishizu uses the Millennium Necklace to see Yami and Tea confess their love for each other.
Yu-Gi-Oh! Beauty and the Beast 2.0 - Ishizu uses the Millennium Necklace to see Yami and Mana confess their love for each other.
Yu-Gi-Oh! Beauty and the Beast 3.0 - Ishizu uses the Millennium Necklace to see Kaiba and Kisara confess their love for each other.
Yu-Gi-Oh! Beauty and the Beast (Vase) - Ishizu uses the power of her Millennium Necklace to curse Atem and also to watch him as Yami until he turns 21. She then uses it to release her power over him and he reverts back to his original form.
Yu-Gi-Oh! Aladdin - Joey is trapped inside the Cave of Wonders with Tristan when the power of the Millennium Rod is unleased revealing Yami Marik. Yami Marik uses the Rod to enact his powers but is trapped by the item as well. Kaiba gets control of the Rod and gains all the powers, then is tricked by Joey and wishes to become a spirit and gets trapped in the stone tablet of the Millennium Items. After the whole battle, Joey wishes for Yami Marik's freedom and is turned back into his normal self, Marik, and is no longer a prisoner of his own item.
Yu-Gi-Oh! Hercules - Atemu and Mana gave Yugi the Millenium Puzzle when he was younger because he was their child. When he is placed on earth, that's the identifying symbol that make Mahado and Isis realize that he's one of the gods. When he's older, they give the Puzzle back to Yugi so he can find out who he really is.
Yugi Moto and the Duelist's Stone - Every new student at Hogwarts must gain a magical artifact to focus their energy. Anubis gained the Pyramid of Light when he started, and Yugi gained the brother of the Pyramid of Light, the Millennium Puzzle. Also, Isis' magical artifact is the Millennium Necklace, Seto's is the Millennium Rod, and the Millennium Key is used to see what house students will be sorted into.