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The film has three acts, referred to as episodes (a reference to how the original Three Stooges short films were packaged for television by Columbia Pictures).

Act / Episode 1: More Orphan Than Not
35 years in the past, the children at the Sisters of Mercy Orphanage are playing soccer with an old soda can in the frontyard. Sister Mary-Mengele, the meanest and strictest nun in the orphanage, tells them to go inside and do their chores. They try singing "Everybody is Special", but she tells them to shut up and go work. Later, three destructive infants, Moe, Larry and Curly, are thrown in a duffel bag onto the orphanage's doorstep from an unknown person's car. The trio subsequently wreaks havoc in the place, terrifying the nuns—especially Sister Mary-Mengele, who has always hated them.