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.

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.

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.

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.

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.

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

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.

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.