The film is broken up into three shorts a la the original Stooges shorts, but they each form one movie.
Episode One - More Orphan Than Not
It begins at the Sisters of Mercy Orphanage where the children are playing happily until cranky Sister Mary-Mengele (Larry David) tells them to go inside. The children begin to do a song as to why they should keep playing, but the nun cuts them off and tells them to go inside. That's when a car drives up by the orphanage and tosses a gym bag on their front steps. As Sister Mary-Mengele opens it up, two fingers poke her in the eyes, sending her falling off the steps. Another nun comes out and calls for Mother Superior (Jane Lynch) and the other nuns. They see baby Moe, Larry, and Curly, all with their trademark hairstyles. They immediately adore all of them, agreeing to split their time with the boys.
Cut to ten years later where the nuns are now terrified of being with the boys. The boys are attempting to remove a tooth out of Sister Mary-Mengele's mouth until they are told that a wealthy couple is coming, so they go to prepare. The nuns plan to keep the other orphans out so that the couple will take the boys out of the orphanage once and for all.
The couple, Mr. and Mrs. Harter (Stephen Collins and Carly Craig), watch Moe, Larry, and Curly do a little performance to get their attention until a smaller and more adorable boy named Teddy comes in. As the couple makes their final decision, they land on Moe and adopt him. As he is leaving, he says goodbye to Larry and Curly, taking something to remember them by. So he rips off a chunk of Larry's hair, and, since Curly has no hair to rip off. Moe plucks out some of his nose hairs.
As he leaves, Moe already starts to miss his friends. When the Harters tell him that it's his birthday, and he can ask for anything, he asks that they go back for Larry and Curly. They go back, but end up leaving Moe and taking Teddy. When asked why he got sent back, Moe says he couldn't deal with the couple after their supposed talk of chores and cleaning their pool.
Cut to 25 years later, where the trio are now grown up and supposedly doing work, but are really slacking off until Sister Mary-Mengele wakes them up.
Meanwhile, an orphan named Peez visits his sick friend Murph, who laments the thought of being put into foster care like Peez's brother Weezer, since they'd be paid to care for the kids. They feel they'd be better off staying at the orphanage living like the Stooges.
The nuns are visited by a priest named Ratliffe, who informs the nuns of their debt. Sister Mary-Mengele blames the trio for this, and he goes to tell them about this situation. He fins them trying to fix a bell on the roof of their little "wirkshop," but they end up causing more damage by removing the bell from its place, and it falls on the cranky nun (Larry read "Do Not Remove" as "Donut Remover" on the bell tag). They try to help her but only continue falling on her or knocking her out.
They come across the nuns and are informed of the debt, and the trio vows to get the money within the 30 days before the place is shut down. They prepare to go out into the real world while Sister Rosemary and Sister Bernice (Jennifer Hudson and Kate Upton) worry how the trio will fare in the real world, but Mother Superior tells them this moment would've come soon enough. The trio prepare to ride off on a bike made for three as they hook their rope to a truck, but Curly tied the hook to the back wheel and they're all dragged off.
Episode Two - The Bananas Split
The trio look for work by advertising that they need $830,000. They are noticed by Lydia and Mack (Sofia Vergara and Craig Bierko). The former plots to have her husband killed off so she can have his money, and they see the Stooges in action, thinking they've found the men for the job. She approaches them and informs them of the job, and Mack comes out claiming to be the husband by saying he has a condition that he wishes to no longer suffer from, so he asks the trio to smother him in his sleep at night, as a surprise. Instead, Curly tricks Mack into looking away as he pushes him in front of a bus, which hits Mack and sends him flying, getting tossed by a street sweeper (I think that's what they're called), jumped on by a girl with a pogo stick, and finally shot in the leg with an arrow that Larry launched five minutes earlier. Furious, Lydia leaves as the Stooges try and follow, learning that Mack survived all of that, but she kicks them out (literally) before they can offer their services again.
They go to the hospital where Mack is, trying to finish the job. They disguise themselves as a doctor and nurses and look for Mack. They end up in a nursery where they try to change diapers but keep getting peed on. They run and find Mack in a full body cast. They try to get him with dynamite, but he survives that too. The trio escape the cops and jump off the roof of the hospital by grabbing a fire hose, which breaks off, and they land on a man. The man recognizes the trio, revealing himself to be Teddy, the orphan adopted instead of Moe. He says he works with Mr. Harter and that his mother died in a hunting accident. He invites the trio to stay with him, but Moe declines. Teddy still invites them to his anniversary party and takes a pic of them. Larry and Curly get mad at Moe, thinking Teddy could've helped them with the money, but Moe says they'll use some money that Mother Superior gave them to start up a farming business. At home, Teddy shoes his wife, revealed to be Lydia, a picture of the Stooges, and she recognizes them, saying he should definitely invite them to the anniversary party.
What the trio really does is try raising fish on a golf course and watering them like produce. They are chased by the cops again and stumble into a building. Larry and Curly argue with Moe about his actions, and eye-poking, stomach-thumping, and head-bopping ensues. Larry and Curly leave Moe alone, and an audience is revealed, applauding Moe for his "skit." The executive (Isaiah Mustafa) offers Moe a spot on the #1 rated reality show.
Final Episode - No Moe Mister Nice Guy
Larry and Curly are still looking for money, but they have no luck. They decide to go to the zoo, where Curly catches fish from the polar bear tank. The duo are spotted by Lydia and Mack, who plan on shooting them. She tries helping him climb into the zoo, but he falls into a lion cage. However, the lion is chained, and Mack stupidly taunts him and smacks him.
The duo try giving a dolphin a peanut, but it gets stuck in his blowhole, so as they try to get it out, Curly launches it out of the hole, and it ricochets to the lion's cage, hitting him in the groin and giving him the fury to break the chain and attack Mack.
Meanwhile, Teddy watches Moe on "Jersey Shore" where he is nicknamed Dyna-Moe. The cast (Snooki, Ronnie, Sammi, JWoww, and The Situation) mock Moe, who uses his eye-poking and head-bopping on them.
The duo goes to find Mr. Harter to ask him for money, but he can't give it to them unless they want to sue the orphanage (or anybody else). That's when they learn how Moe wouldn't go with the couple unless Larry and Curly went with them, and they realize how much Moe cared. The duo suddenly see a picture of Lydia, Teddy, and Mack, and learn from the secretary that Teddy is the husband they were going to kill.
Larry and Curly go to the orphanage, which is practically empty. They find Murph who is really sick and can't go to a hospital because they have no medical insurance thanks to the antics of the Stooges. That's when they see Moe on "Jersey Shore" continuing to inflict pain upon the cast, like eye-poking Snooki and putting Ronnie's head in a microwave.
The J-Shore cast complain to the producers and executive about Moe and learn that they're only still up because of ratings. Larry and Curly bust in, catching the eye of the executive, and getting Moe to come back with them to stop the murder plot.
They go to the anniversary party and continue wreaking havoc by causing a little girl to float away on balloons, dirtying up the food and beverages, and playing with lobster. They are spotted by Lydia and Mack, who try and catch them. They try warning Teddy, who is groggy and still in pajamas, but Mack and Lydia come in and pulls a gun on them. However, Mr. Harter comes in and appears to stop this, until he also pulls a gun on them, revealing him to be the mastermind of the scheme. He and Lydia take Teddy, Mack, and the Stooges with them to finish the job.
As they are driving, Harter reveals that since his wife left the money to Teddy, he would need to die for him to get it. Curly starts laughing as he is tickled by his pet rat that he's been carrying through the entire film. It freaks out everyone, and they drive into a lake. They seem trapped until Moe lights a waterproof match as Curly passes gas, sending them back to the surface.
Lydia, Mack, and Harter are arrested, and Teddy asks the trio what he can do for them. When they ask for the money to save the orphanage, he refuses since the nuns sold him to a man who tried to kill him.
The trio goes back to the now-condemned orphanage, defeated. Suddenly, they hear laughter and splashing, and discover the orphans and nuns playing and relaxing, as it is now an orphanage and spa. The nuns and orphans welcome the trio back as heroes. They're confused, thinking they failed to get the money, but it turns out the money that Moe made from "Jersey Shore" was enough to pay them back. The executive comes out and offers the trio a spot on their new show "Nuns vs. Nitwits", which they happily agree to. Suddenly, Murph comes out looking good as new, saying she just had metal poisoning (Larry had said earlier there was too much iron in the water). That's when Teddy and his new fiancé, Ling the secretary, come to adopt Murph, but she won't go without Peez, so Teddy says they'll adopt both of them, along with Peez's brother Weezer, who they sprung from foster care. The trio feels proud of themselves for having everything go right, until Curly leans on a raised diving board, knocking Sister Mary-Mengele into the pool. They all run away, bouncing off trampolines and onto horses, riding into the sunset.
The film concludes with two muscular guys playing the Farrelly Brothers explaining the stunts and props in the film were done with rubber materials, and demonstrating their used, as well as how they Stooges eye-poke without hurting anyone. They advise children not to try this at home.
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