The Girl Squad were the minions of Margie, who wield Girlifying Rifles that can turn any boy or thing hit by it into a girl and or girly things. The squad was founded by Madam Margaret, Margie's future self, in an alternate future inhabitated by girls. The girls in Madame Margaret's army hate boys, and enjoy frightening and 'executing' innocent boys and often throw insults at the Boys Next Door operatives when battling them. They are also known to cry whenever there is an emergency. In response to the boys' jet packs they have fairy wings. They are much more powerful than the BND. In defense, the girls use heavy heart-shaped cannons that are much faster than regular weapons.
In Operation: F.U.T.U.R.E., at the present day, after Numbuh 4 destroyed Margie's Girlifying Rifle, Madam Margaret used her time machine to provide four girls of the Girl Squad to Margie in order to transform Numbuh 4 into a girl and erase him for her future. The present Numbuh 4 managed to use a jetpack to escape from the Margie's office at St. Rita's Preparatory School, but his jetpack was girlifyed by the Girl Squad's Girlifying Rifles. Still however, Numbuh 4 somehow escaped, but failed to save his friends (as Sector V, with the exception of Numbuh 3, was girlifyed) and was defeated by Margie.
75 years later, Margie, now known as Madam Margaret, is the ruler of a dystopian utopia in which only girls live, girlifying boys or executing them. However, Numbuh 4 created the Boys Next Door, a resistance which was proposed to finish up with Madam Margaret's tyrannical government. One member of the Girl Squad, Sally Sanban, betrayed the squad and Madam Margaret and gave a Girlifying Rifle to the BND. For this reason, after Numbuh 2's descendant altered the rifle's use, she and a now old Numbuh 4 managed to infiltrate in Margaret's walking robotic palace. During the final battle of the Girl Squad agains the Boys Next Door, two girls of the squad were transformed in boys (although it's presumed that they were later transformed baci again into girls) and all the BND operatives were transformed into girls (although it could be possible that some managed to escape as some of the operatives were seen in their secret hangar). However, Numbuh 4, with the help of Sally, managed to use Madam Margaret's time machine to got back to the past, which was later destroyed by Sally, effectively sealing the fate of Madam Margaret and the Girl Squad.
Back to the present day, the older Numbuh 4 warned in time Sector V and they managed to rescue Numbuh 4 in time. Following the rescue, Numbuh 3 used the H.I.P.P.I.E.-H.O.P. to reach Margie's office in St. Rita's Preparatory School. As the four Girl Squad members escaped to a safe location as the Girlifying Rifles were not useful against the H.I.P.P.I.E.-H.O.P., Margie tried to contact Madam Margaret in order to help herself and evade her fate, but Numbuh 3 destroyed the machine and informed her about her sentence for her crimes. Subsequently, the alternated dystopian future was erased and the Girl Squad's four members dissapeared, leaving a weeper Margie alone.
It's completely unknown how Margie's defeat in the past affected the Girl Squad's existence, although it's very likely that the Girl Squad was erased from existence as Margie would not be able to create the squad because she would be captive at the Kids Next Door Arctic Base. Whether this altered their members' lineages or avoid their births is completely unknown.