The Marvelous Misadventures of Flapjack follows a young boy named Flapjack who was raised inside Bubbie, a talking whale. After Flapjack rescues a shipwrecked crusty old pirate named Captain K'nuckles, the misadventures begin. The pair set sail in search of the magical Candied Island filled with lollipop trees and lemonade springs and troublea
Captain K'nuckles accidentally gets Flapjack stuck in a jar when trying to get some Candied Island candy. This leads Flapjack to go on a long journey in an attempt to return home, after being being washed out to sea.
Flapjack and Captain K'nuckles can't escape the Dock Hag's house, after a feeble attempt at destroying K'Nuckles dock tickets, only to discover that the Dock Hag has a crush on the pirate.
After an argument involving Bubbie's tooth door, Flapjack and Captain K'nuckles decide to swap lives for the day, in order to see whose life is more difficult.For K'nuckles who's dressed as Flapjack, he ended up framing the real Flapjack by do nefarious deeds.
Flapjack and Captain K'nuckles take in a rich stranger and hope to profit from their kindness so they can pay off their dock tickets and be able to return to the Harbor.
When Flapjack and Captain K'nuckles are stranded on the moon after getting chased by Eight-Armed Willy, they discover that it could lead them to the long sought-after Candied Island.
Captain K'nuckles avoids being counted in a census being done by Flapjack, due to being ashamed of his inability to count to the number four, which helps save the day.
When Flapjack helps Captain K'nuckles look for his lost hat on an island filled with chimpanzees, they end up encountering a researcher that lives among the animals. With her help, they must reach the "secret meeting place".
Flapjack tries to break Captain K'nuckles of his candy addiction after he develops candy rot. After several attempts to keep him away from sweets, Flapjack and Bubbie send K'nuckles into the sea on a raft.
K'nuckles longs to enter the VIP area of the Candy Barrel.
Flapjack may have a problem with cuddling to much.
Captain K'nuckles becomes unhappy with his own body image, and his problem is compounded when a more beautiful, more rugged adventurer appears and begins to allure Flapjack away from Captain K'nuckles.
Captain K'nuckles has grown tired of Bubbie ending her imaginary tales with a happy end to them, so Captain K'nuckles decides to take Flapjack on a trip to find a story with an unhappy end. When that fails, Captain K'nuckles decides to come up with an unhappy ending story by himself. But Captain K'nuckles may find out that he's biting off more than he can chew.
Bubbie is jealous of K'nuckles' new boat after Flapjack and K'nuckles buy it for only one pence. Bubbie gets jealous because Flapjack and K'nuckles would use it rather than ride on her. Unfortunately, Baron Berserker is on the loose.
Flapjack keeps an eye on Candy Wife while Peppermint Larry is out of town. Unfortunately, Captain K'nuckles starts to play tricks on Candy Wife, until he tells Flapjack he will marry Candy Wife.
Tired of Bubbie always questioning his authority, Captain K'nuckles decides to locate the ship where his Captain's papers are stored, and show them to Bubbie so that she will finally know that Captain K'nuckles is for real! But on the ship, Flapjack and Captain K'nuckles find out something neither of them ever expected, and they also find out that they might not be alone on this sunken ship!
After K'nuckles bets Peppermint Larry that he could eat an entire jar of candy, and wins, one of the customers bet on Flapjack after he gets tired of hearing him say "adventure" when he comes in the Candy Barrel. If Flapjack loses the bet on capturing Eight-Armed Willy, Flapjack is forbidden to say the word "adventure" ever again.
When Bubbie gets a stomach ache, Flapjack must make the dangerous journey into her stomach to fix her.
Mind the Store, Don't Look in the Drawer: Dr. Barber leaves Flapjack and K'nuckles to look after his shop, with one very important rule.
K'nuckles and Flapjack visit a storytelling club, where K'nuckles finds out that his own stories may be outdated.
Flapjack tricks K'nuckles into believing that there is a sea monster attacking Stormalong.
Flapjack gets invited to a birthday party, but feel embarrassed when the other kids perceive K'nuckles and Bubbie as 'weirdos', including for himself.
Flapjack pretends to be a dog for Lady Nicklebottoms while K'nuckles finds the actual dog. However, after Flapjack and Lady Nicklebottoms have such a good time together, Charles (Nicklebottoms' butler) gets jealous and attempts to throw Flapjack into the sea. Meanwhile, K'nuckles experiences the joys of owning a dog.
In the first half-hour long Christmas special, Flapjack celebrates "Low-Tides Day" and awaits his gifts from Poseidon, while K'nuckles tries to find a hidey hole from being sacked by mermen for being a bad kid.
Bubbie kicks K'nuckles out, and Flapjack tries to reconcile the two.
When the fat police constable creates the first bicycle in Stormalong, Flapjack and K'nuckles find it difficult to get away with mischief, especially when the constable begins to abuse his authority and punish them severely for minor offensives.
Bubbie (and eventually K'nuckles) tries to rescue Flapjack from an old woman who thinks he's a missing child.
Sally Syrup returns to Stormalong, much to her disliking and Flapjack must convince her that Stormalong is not all that bad.
When K'nuckles wins a contest for being Stormalong's laziest man, the original owner of the title gets revenge by kidnapping Flapjack.
Flapjack and K'nuckles attempt to befriend two old men who possess a treasure chest from Candied Island.
K'nuckles is bullied by a group of sailors in the Candy Barrel and Flapjack tries to convince him he is not a wimp.
K'nuckles and Flapjack get stranded on a strange island and are unable to find the ocean.
K'nuckles and Peppermint Larry make a bet, and the winner receives a kiss from Candy Wife.
K'nuckles' wish that everyone in Stormalong would disappear comes true, but soon begins to regret making his wish.
Flapjack enters the navy, only to find it's not exciting as he thought it was.
K'nuckles becomes infested with termites.
Flapjack becomes upset when his picture appears in the paper.
Flapjack tries to help Lolly Poopdeck get respect.