Mario, Luigi, and Ben must find Ben's pet who was lost in the sewers while traveling with Captain LardButt in the sea.
The blooper starts with Mario and Luigi riding an ice cream truck to go plumbing some toilets. Mario becomes angry at Luigi because he was dragged in plumbing and Luigi says that it's OK rather than eating spaghetti at the castle all day. Mario asks Luigi why they're even using an ice-cream van instead of other vehicles. Several Gourmet Guys go chasing after the ice-cream truck because they think they sell ice cream.
Mario shouts at Luigi as they see a small Goomba on the road. Luigi quickly turns the ice-cream truck back and it starts rolling on the streets, while Luigi continues screaming and Mario gets happy. The truck rolls into a Warp Pipe and comes crashing next to X's house. Mario says to Luigi if they are finished plumbing they should just go home. Luigi agrees. Mario throws a toolbox at the door and shouts that they are there to fix their pipes and raid their spaghetti.
When the door opens, Ben appears and the two are surprised. Ben asks them if one of them was the male bride that he just bought and Mario says yes. It was Luigi. X goes to the door and says to Mario that they should just ignore Ben because Ben is "really retarded" and pushes Ben inside. Luigi says that they came because they can fix any pipe problems, to which X says no, because they don't have any pipe problems.
Mario gets angry and breaks in through the window. He says to X that he wants to go home but Luigi wants him to fix the pipe. X lets them fix the toilet and says they would just get out of his house when they're done.
Mario clogs the toilet by putting a Toad doll, a banana, a wrench, and Waluigi's rubber ducky, much to Luigi's annoyance, leading to the green plumber deciding to get out of bathroom and get the vacuum. While searching for the vacuum, Luigi sees a squid inside an aquarium and Ben appears right in front of Luigi's face, scaring him. Ben shouts at Luigi and says if anyone touches his pet squid named Mr. Squidge, he will rape him or her. X warns him to just don't touch Ben's "wife". Luigi goes to the toilet room and sees Mario putting a Bob-omb inside the toilet to take out the clog, but the explosion of the bomb causes causes Mario to be flown away. He ricochets on a wall next to a window, and then hits the aquarium, causing Mr. Squidge to escape and stick onto Luigi's face. Mario pulls Mr. Squidge off, making it jump into the toilet.
At this moment, Ben notices Mr. Squidge had disappeared from the aquarium, and then becomes angry and opens the door to throw a chainsaw at Mario. He dodges it and the two go inside the toilet. Then they end up in the sewers. Mario doesn't want to get the squid back with Luigi as he said it's more pain in the @$$. Then a pirate appears right next to Mario with a cutlass, causing Mario and Luigi to panic. He tells them if they don't tell him what they're doing in his "territory", he would have their butts cut off.
This leads Mario and Luigi to start screaming not to do it. Then Ben appears randomly and says they were here to find Mr. Squidge. The pirate thinks Ben meant the Legendary Squid he was searching. However Ben tells him it's his pet squid. Mario calls Ben a little $#!t and says that "[he] doomed us all". This leads Ben to take out his chainsaw again. The pirate tells the Bros. and Ben they are now on his crew to find the squid monster. Mario and Luigi get even more disappointed and Ben becomes excited. The pirate tells them his name is Cap'n Lardbutt and shows them his boat. Luigi notices a bucket, in which Larrbutt says that it is the pooper. Luigi reacts by pushing Ben off the boat.
Prior to leaving the sewers, Lardbutt asks is anyone wants to hear scary pirate stories. Mario responds that he rather sing stupid pirate songs. Lardbutt responds by singing "You are a Pirate," in which Mario collapses. 10 minutes later, everyone are having a fun time except Mario, who is rather annoyed and tells Luigi to stop it. He then tells Ben if they will get out of the boat if Mr Squidge is found. Ben says yes, in which Mario jumps into the water and catches a blooper, but Ben says that the blooper is not his pet. Everyone then searches for Mr Squidge while Lardbutt keeps on catching an orange fish. Mario gives up and says he would rather die. Luigi says the pirate and the passengers need a bigger boat. Ben tries to find a boat to steal, with Lardbutt saying that they at least tried after Ben says he cannot find a good boat. Mario, however, finds a boat on eBay, which appears and falls into the water after Mario buys the ship. Lardbutt reacts to the ship, which possibly means he loves the new ship.
On board the new ship, Lardbutt jumps around. Mario is pissed while Luigi has no idea what is going on. Mario claims the pirate is being constipated and wants to go home. Ben responds by asking about Mr Squidge. Mario responds to this by insulting that Mr. Squidge can suck his hairy ass, then saying that he does not care anymore, which send the two into a fight. Luigi watches, but does nothing except saying "Mama Mia!" Lardbutt likes the new ship and decides to celebrate with a sandwich. However, the two arguing people hit him, which results in him losing his sandwich. The two face the pirate, with Mario responding that Ben did it. Lardbutt then goes after Ben, then a troll face appears on Mario, which shows it is possible that he lied.
At night time, Ben is tied into a rope while Lardbutt tells Mario and Luigi how he became a pirate. Mario likes the story, but he tells him that he doesn't give a crap and wants to go home. Lardbutt replies that he never needed help finding the monster. He also tells Mario he will never get the "Pirate Booty." Lardbutt and Mario argue, until Mario goes naked, making Luigi go"damn!" and Lardbutt stepping back, shocked to see Mario naked. Mario celebrates, saying he has the pirate booty until lightning strikes him. All of a sudden, clouds form, and the earth begins to rumble. Mario asks what is going on, in which Lardbutt responds that the legends were true. The legend was "when tee full moon glows and the ultimate booty shows, the monster appears". The monster is revealed to be Gooper Blooper, who then appears in front of the ship, scaring Mario and Luigi.
When he hears the two scream, Ben asks about the monster's appearance. After he asks, the monster then grabs the ship, tilts it from side to side and then lifts it up into the air, with Luigi hanging on the steering wheel. Mario then decides to fight the monster by throwing a bomb-omb, but it does not work. He then tries the Waluigi Launcher, but it also fails. Mario then tries everything else possible in attempt to defeat the monster. He then goes looks to Lardbutt for other solutions, in which the pirate replies that Gooper Blooper cannot be defeated from the outside. Ben, on the other hand, is interested in the giant blooper monster.
Gooper Blooper them aims for Ben and shoots another blooper. When it passes Ben, it falls back down, in which the trapped toad realizes it is Mr Squidge. Realizing this, Ben untied himself from the rope and falls towards Gooper Blooper. The monster swallows him, choking during the process. Mario is then seen holding onto Lardbutt, who tells him to let go of himself. The ship, however, due to Gooper Blooper choking on Ben, he dies, making the ship fall back into the water. Luigi falls on his back, while Mario asks, "is it over?" Lardbutt sees the monster is dead, in which the sky finally clears up. Ben, on the other hand, is reunited with his lost pet. Mario, Luigi and Lardbutt stare at him. Lardbutt replies, "Well...tis be a crap pirate story..."
Lardbutt finally lets the other three go, and waves a final good-bye. He also warns them not to come near his sandwiches again. Mario also says good-bye, in which it is shown that Mr. Squidge is stuck on the back of Luigi's head. Mario also asks Luigi what to do with Gooper Blooper's corpse.
Back at the house of D, Mario announces that he and Luigi successfully clogged and unclogged the toilet. X just replies with a pathetic "woo-hoo." Mario also tells him that if he sees anything lying around, it was Ben's fault. The two then leave before X can ask a last minute question. Mario also asks him not to sue, in which the truck then crashes into an unknown object. X wonders about what they were talking about, in which he notices the corpse of the squid monster on top of his house. Ben then replies by saying "yay!"