The Stepford Cuckoos were five identical mutant sisters who enrolled at the Xavier Institute and soon proved to be the crème de la crème of Emma Frost's telepathy class. When the Institute was attacked by the mutant-organ-harvesting U-Men, the Cuckoos were among the students that helped oppose them. Later, the Cuckoo Esme romanced a student named Kato who revealed himself to be Stuff, a spy for the alien Shi'ar Empire's Imperial Guard who had been dispatched to Earth by Cassandra Nova to eradicate mutant kind. Along with Emma and fellow student Angel Salvadore, the Cuckoos were captured, but were able to defeat Stuff and free Emma. With her help, the Cuckoos were able to create a trap for Nova. Their class rival Quentin Quire was besotted with the Cuckoo Sophie, and after he rebelled and fomented a riot at the Institute, the Cuckoos opposed him. Taking the power-boosting drug "Kick" and using the X-Men's mutant-locating device Cerebra to further amplify their powers, they defeated him. While her sisters were happy to be molded in Emma's image, Esme was not, and she secretly usurped control of the Cuckoo's group mind. When Sophie resisted, Esme influenced her death, and influenced the Cuckoos to blame Emma for their sister's death and to leave her tutelage. Esme later telepathically forced Angel to shoot Emma, seemingly killing her. Emma was restored by her X-Men teammate Jean Grey's manipulation of the cosmic Phoenix Force, after which Esme fled the Institute, joining who she believed to be the X-Men's arch-nemesis Magneto. After this faux Magneto, one of the mutant brothers known as Xorn, destroyed the Institute and attacked Manhattan, the three other Cuckoos joined an ad-hoc X-Men team to oppose the imposter. Esme ultimately turned against him and was killed for her betrayal.

The three remaining Cuckoos later resolved their differences with Emma, who subsequently became co-headmistress of the rebuilt Institute. The Cuckoos were placed into Cyclops' Corsairs squad, after which Mindee helped the blind X-Man Gambit defend the Institute from an attack by a reformed Brotherhood of Mutants. The Cuckoos then faced the return of Quire after a splintered Phoenix Force came to the Institute seeking Jean. Quire sought to resurrect his beloved Sophie and asked the Force for help. It restored her to life, but upon seeing Quire she chose to return to death. The Force departed after merging with Jean to search for its missing pieces, one of which later visited the Cuckoos. Recently, when the immovable mutant the Blob attacked the Institute, the Cuckoos were instrumental in his defeat by the students. During the mutant Scarlet Witch's reshaping of reality, the Cuckoos briefly became a quintet once more.

After the effects of M-Day the trilets retained their powers and the small fragment of the phoenix force that came to one of the cuckoos, began to influence their behavior. Being manipulated by both the Phoenix and a man named John Sublime, the Cuckoos awoke their dead sisters and traveled to the World, a laboratory created by Weapon Plus, it was revealed that Emma Frost's ova was the genetic templates used to clone thousands of cuckoos. It was also revealed that the Phoenix fragment had manifested in order to destroy the Cuckoos clones to prevent them from being activated as a weapon and kill all mutants.