Once upon a time in Ghost Central, when the ghostly trios (Stretch, Fatso and Stinkie) are so young, the leader of the Ghos Central named Kibosh interduce the ghost students to a beautiful female ghost name Queen Bugaroo. Kibosh told all ghosts to make her feel welcome and she'll make a wonderful scared someone that are humans. But Queen Bugaroo is not so good ghost she'll plan to get rid of the ghostly trios. The ghostly trios are finding out that is Queen Bugaroo up to and they find out that she is evil but Queen Bugaroo called her insects army to trick the trios by fighting her.
When Stretch stretched his arms to get rid of the insects they bite him. When Fatso tried to eat any insects they keep flying around him. But Stinkie is smart enough to stink any bugs. But when Kibosh came Queen Bugaroo lies to him that the ghostly trios are playing mean ghost tricks on her but when when the ghostly trios begs Kibosh the truth he told them that they are expelled for treating her that way so banished them to the human world. Now Queen Bugaroo can never see them again because her evil plan. The ghostly trios saws the sign said "Welcome to Deedstown" and they fly around and people are so scared of ghosts. That gives Stretch an idea if the ghostly trios trains themselves to scare people they'll provide Kibosh that they're the best scary ghost in the world and they promise each other to forget about Queen Bugaroo.
Years later after the ghostly trios adopted a little ghost name Casper as their nephew (like in Casper: A Spirited Beginning) they can't let him know about Queen Bugaroo because they never mansion about her for a long time ever since she got them expelled. Every time they teach Casper to scare fleshy but he wants to make friends with them because his uncles don't want him too. That morning the ghostly trios told Casper to scared the old lady but when he says hello to her the lady looked up and she saw a ghost and then she ran away and then the ghostly trios scared her too. But Casper really need a friend to play with him.
Meanwhile in the underworld Queen Bugaroo is so glad that she the best scary ghost in the world. But her little insects friends told her in the human world the ghostly trios are the best scary ghost in the world and then Queen Bugaroo is so frustrating because they are still around as some ghosts. So she decided to get rid of the ghostly trios again just like she got them expelled. Queen Bugaroo asked her insects army to help to destroy the ghostly trios and then with them out of the way she will be the best scary ghost in the world.
Back at Deedstown, in Applegate Mansion, the ghostly trios are watching a scary movie about when some people are afraid of ghosts during that they have to talk about Queen Bugaroo but Stretch told Stinkie and Fatso that they all promise to never mansion about her and they were afraid to tell Casper about her because if the ghostly trios tell him about Queen Bugaroo he'll run away and that why they'll keep it to themselves. But Casper remember all those years of how much friends he'll make. Then he got very tired so Casper decided to take a nap and fall asleep.
Outside of Applegate Mansion, Queen Bugaroo told her termites to tear down the house and they did. The ghostly trios saws the termites are tearing down everything in their home so they fly away but they forgot Casper who's already asleep in his room. Stretch fly back and grabbed Casper and carry him back outside. The ghostly trios saws the termites tears all of Applegate Mansion Stinkie and Fatso wonder if all those termites are working for Queen Bugaroo but Stretch told them that they were supposed to forget about her and they understand that and then they fly away with one of them holding Casper in their arms. Queen Bugaroo is watching the ghostly trios are flying away from her but she'll get them yet.
The ghostly trios set out the camp in the woods while Casper still napping and they bailout a campfire. They still don't know why that Queen Bugaroo had them expelled from Ghost Central for her evils tricks because she made them fight with her and that they never mansion to talk about Queen Bugaroo again. Then suddenly Queen Bugaroo came and surprised to see the ghostly trios again, Stretch began to fight against her while Stinkie and Fatso carry Casper to keep away from Queen Bugaroo so she won't go near him. During this Queen Bugaroo's insects army came and try to attack them, when Fatso tried to eat some of them they're too easy to be catch so Stinkie told Fatso to hold Casper while he used his smells to stink all of the insects and he did.
Meanwhile when Stretch try to fight Queen Bugaroo back she was so easy on him but Stretch stretched his arms to punch her in a face then Queen Bugaroo got so angry so told Stretch that she'll be back to play more games on him and his two brothers and then she left. When Stinkie and Fatso came back with sleeping Casper and saw Stretch so mad and he told Fatso and Stinkie if they get their hands on Queen Bugaroo they'll stand up to her and scared her. As soon Casper wake up and saws his uncles are fighting about if Queen Bugaroo haven't expelled them everything would be fine. Casper demand his uncles to tell him the truth about Queen Bugaroo and they told him everything that she got them expelled and they were so afraid if the ghostly trios tell Casper about her he would run away. Casper was not too happy because the ghostly trios didn't want him to know about Queen Bugaroo so he fly away from them and then the ghostly trios are so sad for what they'd done.
Casper was so mad because his uncles keep it screct from him and he was feeling sorry for himself because he was so angry at his uncles. Then suddenly Queen Bugaroo arrived and began to pick on Casper, he asked her why did she got the ghostly trios expelled from Ghost Central, Queen Bugaroo told Casper that she is so jealous of them and she didn't like them at all. When the ghostly trios are trying to look for Casper they saw Queen Bugaroo is playing mean game on him so the ghostly trios fly up to stop her to save him. The ghostly trios demand that Queen Bugaroo to stop playing games on Casper immediately, but she refused so she use her spider web to rapped the trios up and catching them. The ghostly trios told Casper to run and he did but Bugaroo told her insects to go after him but they couldn't find him and then Casper needed to get help so fly to he find his old friends immediately.
Meanwhile Queen Bugaroo has taking the ghostly trios to her lare and untie them. Stretch demand that Queen Bugaroo to let him, Stinkie and Fatso go immediately. But Queen Bugaroo is refused by not doing so. Fatso told her that little ghost she pick on was the trios nephew but Queen Bugaroo was frustrating because she hate children so she decided to traps the ghostly trios in the giant glass of jar to make them how long she'll keep in there until the trios get unconscious. The ghostly trios are trying to use their cents to get them escape but the jar is too strong for them now.
Casper fly around the world to find his friends, first he found his two friends from Scare School, Ra the mummy and Mantha the zombie whose can him to save the ghostly trios, then they found Casper's old girlfriend Wendy the good little red witch who will use her wand to help and finally they found Casper's cousin, Spooky and his girlfriend Poil whose also like to help too. Casper told Spooky, Poil, Wendy, Ra and Mantha that the ghostly trios never told him about Queen Bugaroo for a long time and he shouldn't be so rude to them before they got catcher by her. Ra and Mantha told Casper that they know a pirate who can help them to save the trios and his named is Cappy the pirate and his parrot Beaky whose can drive the flying ship to come to the rescue.
Back at Queen Bugaroo's lare she was so frustrating because a friendly ghost had found an army to help him rescue his uncles. The ghostly trios demand that Queen Bugaroo to never get away with this, she told them that she already has. The ghostly trios are so scared because they lost Casper while they were kidnapped and they'll be unconscious in any minute in the giant jar.
Meanwhile Casper, Spooky, Poil, Wendy, Ra, Mantha, Cappy and Beaky had fly the ship to Queen Bugaroo's lare and they hope she doesn't do anything harm to the ghostly trios. Then suddenly Queen Bugaroo and her insects army came out and try to harm Casper and his friends. Casper demand that Queen Bugaroo and tell her where are the ghostly trios, Queen Bugaroo told him that she trapped them in the giant jar to make them unconscious. Casper told Wendy, Ra, Mantha, Cappy and Beaky to fight Queen Bugaroo and her army immediately while he, Spooky and Poil went inside the lare to find their uncles.
Casper, Spooky and Poil came inside and found the ghostly trios trap in the giant jar and they were finding away to get out of there. The three little ghosts work together to open the lids to free the ghostly trios and they did. The ghostly trios are so glad that Casper, Spooky and Poil have come to rescue them, while Wendy, Ra, Mantha, Cappy and Beaky are battling Queen Bugaroo and her insects. Wendy use her wand to destroy the insects, Ra use his part of his rap to rapping the insects, Mantha use her head to knock the insects unconscious, Cappy use his sword to fight off the insects and Beaky use his beak to eat all the insects.
Later Casper, Spooky, Poil and the ghostly trios came outside and Queen Bugaroo was so frustrated because Casper has the ghostly trios escape so she decided to destroy them. But Casper have an idea so told Wendy to vanish Queen Bugaroo in the Abyss just like what the evil warlock was trying did to Wendy, so she used her wand to open the the Abyss and then Stinkie use his smells on Queen Bugaroo and then she falls into the Abyss and then Wendy use her wand to close the Abyss. Later Kibosh came and told Casper and the ghostly trios how did this happen. Casper told Kibosh that the truth is that Queen Bugaroo was trying to get rid of the ghostly trios just like she got them expelled for her evil plan. Kibosh didn't realize that Queen Bugaroo hated the ghostly trios so he was wrong to expelled the trios and he told them that they're the best scary ghosts in the world and then left.
After that Casper thanks Spooky, Poil, Wendy, Ra, Matha, Cappy and Beaky for helping him saving his uncles from Queen Bugaroo so Spooky and Poil fly back to New York, Wendy give Casper a kiss and then fly on her broomstick back to her three aunts and Ra, Matha, Cappy and Beaky took a flying ship and fly back home. After they say goodbye to Casper and the ghostly trios, they fly back to Deedstowns and rebalt their new mansion called Whipstaff Manor and they all live happily ever after.