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.

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.

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 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.

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.

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.

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.

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 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.

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.

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

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.

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.

Sally Syrup returns to Stormalong (much to her dismay) and Flapjack must convince her that Stormalong is not all that bad.