Season 2

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.

Flapjack and Captain K'nuckles struggle to escape from the Dock Hag's house after a feeble attempt at sabotaging K'nuckles' dock tickets, only to discover that the Dock Hag has a crush on the old captain.

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.

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.

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 Candied Island. All they need to do is trick the moon (who, they discovered, has a mind of its own) into taking them there.

Captain K'nuckles refuses to take a census conducted by Flapjack, due to a misunderstanding. Unfortunately, the census takers who assigned this duty to Flapjack are actually a group of pirates wanting to take over Stormalong.

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.

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

K'nuckles needs to get fancy pants to get into the new VIP section of the Candy Barrel.

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

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

Tired of stories with happy endings K'nuckles and Flapjack go off in search of a story without one, but their imaginations quickly run wild.

Bubbie becomes jealous of K'nuckles' new boat, while unbeknownst to the trio, the boat's original owner seeks to kill Flapjack and K'nuckles.

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

K'nuckles tries to prove he's a captain by visiting a sunken ship to collect his captain's papers.

Flapjack has to capture Eight-Armed Willy to prove he is worthy of being a real adventurer.

When Bubbie gets a stomach ache, Flapjack must go on a dangerous journey into her stomach to fix it.

Dr. Barber leaves Flapjack and K'nuckles to look after his barbershop/clinic with one important rule: they must not open a drawer. As a result, they are very curious about what is in the drawer.

K'nuckles and Flapjack visit a storytelling club, where K'nuckles finds out that his own stories may be outdated.

When Flapjack pulls a sea monster-related prank on K'nuckles the citizens of Stormalong banish him from the harbor by throwing him into the ocean, leaving Flapjack to try to get him back.

Flapjack gets invited to a birthday party, but feels embarrassed when the other kids perceive K'nuckles and Bubbie as "weirdos".

Flapjack pretends to be a dog for Lady Nicklebottoms, while K'nuckles experiences the joys of owning a dog.

Flapjack celebrates Low Tide Day and awaits his gifts from Poseidon, while K'nuckles tries to find a place to hide from the mermen for being a naughty person.

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.

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 dismay) 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 are stranded on a strange island and are unable to find the ocean.

K'nuckles challenges Peppermint Larry to a game of pool to settle the ownership of Candy Wife.

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

Flapjack joins the navy to prove K'nuckles he has a life, only to find it's not exciting as he thought it was.

K'nuckles becomes infested with termites.

Flapjack becomes upset when an embarrassing picture of him appears in the paper.

Flapjack tries to help Lolly Poopdeck get respect when he gets tired of being a laughingstock.

There are dire consequences when Flapjack switches places with a sailor.