Blair Flannigan, known in the original Japanese version as Rei Saotome, is a determined young duelist who becomes an unexpected presence at Duel Academy. She is initially an underage student and, for a time, the only female resident of the Slifer Red dormitory. Blair first appears during the first year at the academy, introduced as a transfer student who is secretly in disguise as a boy. Her primary motivation at this time is not academic; she has an intense crush on the top duelist Zane Truesdale and infiltrates the academy to get closer to him. Blair is highly intelligent and performs exceptionally well on her entrance exams, nearly qualifying for the Ra Yellow dorm.

When Blair is caught sneaking into Zane's room in the Obelisk Blue dorm, her secret is discovered by Jaden Yuki. To ensure his silence, she duels him. Although she loses the duel, she finally gets a chance to confess her feelings to Zane. Zane is flattered but turns her down, pointing out that she is too young to be a student. In the English dub, she is stated to be eight years old, while in the original Japanese version, she is a fifth-grade elementary student, making her approximately eleven. Forced to leave the academy, her affections unexpectedly shift from Zane to Jaden as she departs, much to his dismay.

Blair returns near the end of the second year during the Genex Tournament. She has matured significantly and her skills as a duelist have improved dramatically. She challenges a changed Zane, who declines, and instead duels Chazz Princeton for the right to enroll in the Slifer Red dorm officially. Her dueling style has evolved, and she now uses an Egg Deck, which focuses on monsters like Mystic Egg that evolve through different growth stages. Although she pushes Chazz into a corner, she ultimately loses, but is still admitted to the academy. Her personality becomes more defined during this period; while her love interests seem to shift, including a brief admiration for Chazz, her enduring crush on Jaden remains a central and recurring trait.

At the start of the third year, Blair becomes a more prominent member of the main cast. She joins Slifer Red, commandeers Chazz's room, and tries to befriend a quiet student named Marcel. When Duel Academy is transported to an alternate dimension, she is attacked by the entity Yubel and falls mysteriously ill. Her friends secure medicine for her, and she recovers. Later, she witnesses the possessed Marcel dueling Jaden and Jesse. Demonstrating her compassion, she demands that Yubel release Marcel, which it does, and she catches the unconscious boy.

By the fourth season, Blair has been promoted to the Obelisk Blue dorm, though she continues to wear her red jacket. She participates in a Tag-Team Duel tournament partnered with Tyranno Hassleberry. During a tag duel against Jaden and Alexis, she uses a card to switch partners, hoping to team up with Jaden due to her persistent crush on him. She briefly duels alongside him before Alexis undoes the switch, leading to Blair's defeat. In the final arc, she is among those absorbed into the World of Darkness but is revived after Jaden defeats the villain Nightshroud. Upon her return, she immediately runs to embrace Jaden.

Blair is a recurring character in various video games. In Yu-Gi-Oh! GX Tag Force, she uses a Serene Silence Deck with Silent LV monsters before switching to a Maiden in Love Deck. In later games, she is depicted using a Lightsworn deck. Her most notable abilities as a duelist are strategic and evolve over time. Her first strategy is based on her Maiden in Love card, which distributes Maiden Counters to opponent monsters, allowing her to take control of them. Her later Egg Deck focuses on summoning and rapidly evolving monsters through their life cycles.