After Flapjack brags about Bubbie's speed, he ends up involving himself, K'nuckles, and Bubbie in a race through the Sea of Teeth against an evil inventor and his mechanical Alpha-Whale.

While doing their laundry K'nuckles and Flapjack decide to spy on Bubbie, to find out what she does all day.

K'nuckles bets Flapjack in a poker game, resulting in the two having a falling-out. K'nuckles replaces Flapjack with a young boy named Kid Nickels, while Flapjack becomes a banker's apprentice. K'nuckles ends up missing Flapjack and challenges the banker to win him back.

The evil inventor's twin brother builds a "Grand Flying Contraption" to impress Bubbie, on whom he has a crush. However, when Bubbie does not return the same feelings (she sees him as a friend, rather than a love interest) he becomes very sad. Because of this, Flapjack and crew are inadvertently led into danger.

In a scheme to trade wrappers with Peppermint Larry in exchange for candy, K'nuckles and Flapjack search for a "+" because Peppermint Larry says he will give them 100 pieces of candy in exchange for it.

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.

When Captain K'nuckles believes he has found a map to Candied Island, he wants Flapjack to read it to reach their destination. However, Flapjack (in dire need of a haircut) cannot. They go to Doctor Barber for a haircut, only to find that the barber has stolen the map.

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.

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.

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.

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.

For Flapjack's birthday K'nuckles, Bubbie, and Flapjack sail west in search of Candied Island.

Flapjack adopts a rat he rescues from a flood and names it K'nuckles II, but his new pet ends up infecting everyone in Stormalong with the plague.

Flapjack, Captain K'nuckles, and Bubbie journey to the Bottom of the World to reclaim K'nuckles' long-lost "sittin' muscle" (his buttocks).

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.

After relating a tale that reveals why he doesn't trust women Captain K'nuckles ends up falling in love with his own reflection, believing it to be a beautiful woman.

When Peppermint Larry hosts his annual Adventure Beard-Off Contest Captain K'nuckles enters the contest, with Flapjack pretending to be his beard.

Flapjack finds out Peppermint Larry is preparing for the Stormalong Pun-Off, in which he will compete against comedy legend Punsie McKale. After Flapjack and Larry are knocked out by Punsie's puns, K'nuckles steals the show.

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

Flapjack and Captain K'nuckles get stranded on an island inhabited by a mechanical genie; after fishing for food, they discover that not everything is as it seems.

Captain K'nuckles tells Flapjack that the more enemies an adventurer have, the greater adventurer he is. This results in Flapjack going on a quest to make enemies and all his plans backfiring.

Desperate to find a younger sibling after Captain K'nuckles calls him "a baby" out of annoyance, Flapjack asks Bubbie where babies come from and mistakenly adopts a duck as his new "baby brother".

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.

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.

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 denies he is in love with Sally Syrup, despite the little red hearts that pop up around his head.

Bubbie falls in love with a whale named Harvey, who kidnaps Captain K'nuckles and Flapjack to work in his factory on Laundry Island – unknown to Bubbie, who thinks they are ignoring her.

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.

Flapjack is told by Bubbie the origin of his name before getting his first "special flapjacks". However, Captain K'nuckles forbids Flapjack from eating pancakes without syrup and the two set out to solve the recent syrup shortage.

When Flapjack discovers some fresh fruit (which hasn't been seen in years) and Captain K'Nuckles eats it, the two head to an island to get some more but a mysterious plant man keeps getting in the way.

The Dock Hag catches Flapjack and Captain K'nuckles littering and sentences them to community service collecting fish heads. Doctor Barber offers to pay them for the heads (much to their delight), but they soon discover his true intentions for the fish heads.

Flapjack keeps getting mistaken for a girl so he and Captain K'nuckles attempt to literally "man him up", only to discover that his voice is the problem.

Captain K'nuckles steals a mermaid queen's heart filled with wishes (in the form of candy) so he and Flapjack can go to Candied Island, but they quickly misuse the wishes and learn a terrible secret about the mermaid.

Flapjack and Captain K'nuckles are swindled by a mysterious man named Ben Boozle and are forced to work on his ship until Flapjack can achieve the rank of captain.

Flapjack and Captain K'nuckles sneak aboard a candy cruise ship, but accidentally anger Poseidon when they destroy the ship's figurehead.

Flapjack is dubbed Captain K'nuckles' guardian angel by Bubbie but when Flapjack annoys him with constant protection, K'nuckles fakes his own death to have peace.

When Captain K'nuckles and Bubbie read Flapjack's secret diary, Flapjack decides to live like a hermit on a remote island to keep his secrets safe.

Taunted by a rich boy for being poor, Flapjack and Captain K'nuckles search for diamonds that the rich boy claims are in the sewers of Upper Stormalong Harbor.

Flapjack learns from Captain K'Nuckles about a strange man who trades combs in exchange for candy. After finding the man's family is in a similar situation to his, Flapjack helps the man (Tee Hee Tummy Tums) sell his combs.

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.

When Peppermint Larry falls sick, Flapjack and K'nuckles are forced to go fishing for food.

K'nuckles becomes the new mayor of Stormalong.

When K'nuckles continues to trick people and blame ghosts, Flapjack consults Jayde, the resident ghost expert of Stormalong, to see if ghosts really do exist.

K'nuckles claims he knows where Candied Island is but gets caught up in his lie.

Flapjack makes Doctor Barber a friend out of candy.

K'nuckles gets a new face to avoid a mob after stealing boots but ends up caught in the mob.

The outrageous adventurer Ponce de Lee-Roy convinces K'nuckles he's an immortal.

Flapjack causes an infestation of non-lucky cats in Stormalong, leaving him and K'nuckles to fix the problem.

When a storm hits Stormalong, Flapjack and K'nuckles offer to help the town in exchange for candy.

Flapjack and K'nuckles wreak havoc on civilization in the clouds.

Flapjack tries to clear K'nuckles' name when he is accused of stealing candy.

Flapjack and K'nuckles consume too much of a new drink at the Candy Barrel, and it turns them into fish.