Morgan appears in the Ultimate Spider-Man episode "Halloween Night at the Museum" (a crossover with Jessie). She is accidentally freed from her armor imprisonment at her museum by Jessie Prescott during the Ross Kids visit to the museum as she plans to claim the sword and cause the end of the world. Spider-Man comes to their aid as Morgan le Fay brings the exhibits (consisting of a skeleton, the Tyrannosaurus skeleton, a Triceratops skeleton, two wax caveman statues, a giant earthworm statue) to life while placing a jack-o'-lantern on a security guard turning him into Jack O'Lantern. Following the fight with Jack O'Lantern and the evasion of some exhibits, Morgan le Fay makes another attempt at the sword where she transforms Mrs. Kipling into a dragon.
Morgan le Fay then attacks Jessie as she uses the sword to combat Morgan le Fay. After blasting the sword out of Jessie's hands, Morgan le Fay grabs the sword in order to blot out the sun and become the true heir of Camelot. After Ravi regained control of Mrs. Kipling, Jessie places the sword back onto the armor as Morgan le Fay is re-imprisoned.
Morgan le Fay appears in the episode "Weirdworld" as the ruler of Weirdworld. She allies with Bruce Banner, who had been separated from the Hulk, to destroy Hulk once and for all. The plan is complicated with the arrival of Captain Marvel and Black Widow, who Morgan le Fay manages to capture until Banner finally incapacitates Hulk and brings him to Morgan le Fay. However, Morgan reveals that she intends to absorb Hulk's essence for herself rather than destroy him. Banner then double-crosses Morgan and frees his friends as Morgan le Fay summons minions to fight them. After falling into Morgan's magic chamber, Banner and Hulk are fused back together and overwhelm Morgan le Fay, forcing Morgan le Fay to retreat.
