Captain K'nuckles and Flapjack stow away on a ship that they believe will take them to Candied Island. Instead, they end up on the mysterious Cammie Island; Flapjack befriends the misunderstood (and lonely) monster of the island.

Flapjack and Captain K'nuckles suffer from a severe case of foot burn (sunburned feet) after sleeping in the sun. On their quest to treat it, they discover a hideous trolley driver whom K'nuckles knew from his past.

Flapjack learns to balance a board on the waves (surfing) and becomes Stormalong's biggest film star.

When Bubbie sends Flapjack and K'nuckles to get shelf polish on the "bad side" of town, they get into trouble with a group of alley kids and ultimately are challenged to a dance-off to get their possessions back.

Flapjack finds he may have a problem with cuddling after a night sleeping outside, so he tries to find the cause and a cure.

Captain K'nuckles accidentally gets Flapjack stuck in a jar when trying to get some Candied Island candy. This leads Flapjack on a long journey in an attempt to return home, after being washed out to sea.

When the Dock Hag bans Flapjack and K'nuckles from setting foot on the main harbor until they pay off their tickets, they take in a rich stranger in the hope he will pay them for being such kind friends. However, they rethink their idea when the stranger begins to take advantage of their hospitality.

Flapjack tries to break Captain K'nuckles' candy addiction after he develops a severe case of "candy rot".

K'nuckles is bullied by a group of sailors in the Candy Barrel, and Flapjack tries to convince him he is not a wimp.

After an argument involving Bubbie's tooth door, Flapjack and Captain K'nuckles decide to disguise themselves as each other for the day to see whose life is more difficult.

Flapjack keeps an eye on Candy Wife while Peppermint Larry is out of town, making Captain K'nuckles jealous.

K'nuckles and Flapjack visit a storytelling club, where K'nuckles finds out that his own stories may be outdated.

Bubbie kicks K'nuckles out, and Flapjack tries to reconcile the two.

When the fat police constable (called Constable Norm in later episodes) 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 offenses.

When they assume that Bubbie has been kidnapped by a group of foreign sailors known as the Snarks, Flapjack and K'nuckles sneak aboard their ship to locate her.

When Captain K'nuckles believes he has accidentally cursed Flapjack with the inability to speak he tries to find a cure, only to discover it to be a ruse by Flapjack to attend the local Knot Festival.

When the Candy Barrel is shut down by the Dock Hag due to a misunderstanding, Peppermint Larry tries his hand at puppetry. He eventually finds success with "The Amazing Adventures of Pancake" – a spoof of Flapjack and his adventures, much to Flapjack's dismay.

When Flapjack helps Captain K'nuckles look for his lost hat on an island filled with chimpanzees, they end up encountering a researcher living among them. With her help, they must reach the "secret meeting place": an active volcano whose crater K'nuckles must cross so he can get his hat back.

When K'nuckles refuses to lose weight, he risks losing Flapjack to a real adventurer.

Flapjack and K'nuckles attempt to befriend two old men who possess a treasure chest from Candied Island.

When Flapjack thinks he's unable to tell directions, he and K'nuckles decide to go to school. But K'nuckles finds himself unable to keep up with the other students and later plans to steal the candy rewards that the teacher gives out. However, he finds out something strange about the school.

Captain K'nuckles is accused by a pirate captain of stealing his hand, leading Flapjack to believe that K'nuckles is nothing but a liar. This puts a strain on their friendship, causing everyone else believes that K'nuckles stole from them.

Believing K'nuckles to be a bad influence Bubbie tells Flapjack to stop following the pirate, but to lead him instead. Unfortunately, after taking the advice of an animal trainer Flapjack accidentally hypnotizes K'nuckles into believing he is a seal.

After Flapjack finds a pair of legs adrift at sea, Captain K'nuckles uses them to terrorize the people of Stormalong Harbor. However, when a sea monster's torso comes to reclaim the legs a battle for ownership ensues.

K'nuckles' wish that everyone in Stormalong would disappear comes true, but he soon begins to regret his wish.