Saison 1

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.

Flapjack and K'nuckles befriend the richest lady in Stormalong, Lady Nickelbottoms, to steal from her mansion (which is made from candy). When their plans go awry, K'nuckles finds himself challenging Lord Nickelbottoms in a candy-based duel to the death.

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.