Flapjack tells a crazy inventor that Bubbie is faster than a machine. K'nuckles and Flapjack stow away on a ship and arrive at an island they believe to be Candied Island.
After winning a poker game, Captain K'nuckles ends up losing Flapjack as a friend. Flapjack meets a wealthy old woman, who wants to turn him into proper young man.
Bubbie and Flapjack meet the twin brother of the evil inventor from Several Leagues Under the Sea, and Bubbie tries to help him accomplish his and her dreams of creating a flying ship. However, it would seem that the twin brother is actually in love with Bubbie, leading to one dangerous adventure above the raging sea. Peppermint Larry offers free candy for used candy wrappers, especially the one mysteriously marked X, so K'nuckles abuses Flapjack's trust to get them.
K'nuckles finds a treasure map and needs Flapjack's help to read it, but Flapjack needs a haircut first and the barber steals it. Flapjack spies on Bubbie to learn what she does all day only to discover that she is a peeper.
K'nuckles dimwittingly misleads Flapjack into the mouth of Eight-Armed Willy, not knowing his left from his right. This causes Flapjack to believe it is his fault that they could not navigate the map. He and K'nuckles, instructed by Bubbie, go to school in order to receive an a basic education in navigation. However, a more devious plan is being hatched in the schoolhouse that the adventurers are unaware of. 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. And on their quest to treat it, they discover a hideous trolley driver whom K'nuckles knew from his past. K'nuckles creates tall tales about his prosthetic hands, when a man claiming to be the true owner of his right hand appears. He threatens K'nuckles and demands the return of his hand in 24 hours. Flapjack attempts to save the hand, having complete trust in K'nuckles' story, and finds out that his fellow adventurer isn't the honest sailor that he claims to be. Flapjack confronts K'nuckles about this, and his shouting about the latter's lies leads the citizens of Stormalong to take back what he apparently stole from them, literally tearing him apart and leaving only his eyes left in the end. However, it is soon revealed that K'nuckles was indeed telling the truth about his right hand; it was sold as a back-scratcher, and the man realizes that the "back-scratcher " is his
Flapjack and K'nuckles sail out into the most dangerous direction of all. The wessssst. Flapjack makes all the citizens of Stormalong uncomfortable when he becomes friends with a rat he names "K'nuckles II" while the real Captain K'nuckles is away.
Flapjack and K'nuckles travel to the South Pole in search of a long lost body part. Annoyed at Flapjack's constant noises while he is trying to sleep, K'nuckles tells Flapjack about the curse of Mute Mike and accidentally curses Flapjack with the inability to speak.
Flapjack helps a lonely K'nuckles find love. Peppermint Larry hosts his annual Adventure Beard-Off. Men with fantastic beards compete to win Peppermint Larry's candy-daughter's hand in marriage.
Peppermint Larry is preparing for the Stormalong Pun-Off, where he will compete with comedy legend, Punsie McKale, in joke-telling. Stormalong is visited by an eccentric man promising wonders never seen before. The "wonder" turns out to be a film.
While searching for Candied Island, K'nuckles and Flapjack find an island with a mechanical genie. After K'nuckles tells Flapjack that the more enemies an adventurer has, the more of a great adventurer he is, Flapjack sets out to make as many enemies as he can.
Flapjack attempts to create a brother for himself. When Peppermint Larry loses ownership of his store, Flapjack tries to find him a new job.
Flapjack is told by Bubbie not to follow Captain K'nuckles around anymore and tells Flapjack to lead Captain K'nuckles, only for it to backfire. Flapjack leads K'nuckles like a seal by mistake and K'nuckles turns into a seal. A gang of kids from the bad part of Stormalong pick on Flapjack.
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 and Captain K'nuckles sneak aboard a candy cruise ship, but accidentally anger the Poseidon when they destroy the ship's figurehead, which was of his daughter.
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 occurs. Flapjack is told the origin of his name before getting his first "special flapjacks." However, when Captain K'nuckles informs Flapjack he can't eat pancakes without syrup, so 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, however, 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 man him up, only to discover that his voice is the problem. Captain K'nuckles steals a mermaid queen's heart filled with candy wishes, with the intention of him and Flapjack to get to Candied Island, but they quickly misuse the wishes and learn a terrible secret about the mermaid.
When it is thought that Flapjack has fallen in love with a girl named Sally Syrup, Peppermint Larry and Captain K'nuckles hoping to profit from the arrangement, by stealing the lovehearts that pop out of his head. Flapjack and Captain K'nuckles are swindled by a mysterious man named Ben Boozle, and are forced to work on his ship until Flapjack is able to achieve the rank of captain.
Flapjack is dubbed Captain K'nuckles' guardian angel by Bubbie, but when Flapjack annoys him with constant protection, K'nuckles fakes his own death in order 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 all his various secrets safe.
When taunted by a rich kid for being poor, Flapjack and Captain K'nuckles search for diamonds that the boy claims is in the sewers of Upper Stormalong Harbor. Flapjack learns from Captain K'Nuckles about of a strange man that gives away combs in exchange for candy. Upon finding out that this man's family is in a similar situation as him, Flapjack decides to help 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 to go on a long journey in an attempt to return home, after being being washed out to sea. Flapjack and Captain K'nuckles can't escape the Dock Hag's house, after a feeble attempt at destroying K'Nuckles dock tickets, only to discover that the Dock Hag has a crush on the pirate.
After an argument involving Bubbie's tooth door, Flapjack and Captain K'nuckles decide to swap lives for the day, in order to see whose life is more difficult.For K'nuckles who's dressed as Flapjack, he ended up framing the real Flapjack by do nefarious deeds. Flapjack and Captain K'nuckles take in a rich stranger and hope to profit from their kindness so they can pay off their dock tickets and be able to return to the Harbor.
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 the long sought-after Candied Island. Captain K'nuckles avoids being counted in a census being done by Flapjack, due to being ashamed of his inability to count to the number four, which helps save the day.
When Flapjack helps Captain K'nuckles look for his lost hat on an island filled with chimpanzees, they end up encountering a researcher that lives among the animals. With her help, they must reach the "secret meeting place". Flapjack tries to break Captain K'nuckles of his candy addiction after he develops candy rot. After several attempts to keep him away from sweets, Flapjack and Bubbie send K'nuckles into the sea on a raft.
K'nuckles longs to enter the VIP area of the Candy Barrel. Flapjack may have a problem with cuddling to much.
Captain K'nuckles becomes unhappy with his own body image, and his problem is compounded when a more beautiful, more rugged adventurer appears and begins to allure Flapjack away from Captain K'nuckles. Captain K'nuckles has grown tired of Bubbie ending her imaginary tales with a happy end to them, so Captain K'nuckles decides to take Flapjack on a trip to find a story with an unhappy end. When that fails, Captain K'nuckles decides to come up with an unhappy ending story by himself. But Captain K'nuckles may find out that he's biting off more than he can chew.
Bubbie is jealous of K'nuckles' new boat after Flapjack and K'nuckles buy it for only one pence. Bubbie gets jealous because Flapjack and K'nuckles would use it rather than ride on her. Unfortunately, Baron Berserker is on the loose. Flapjack keeps an eye on Candy Wife while Peppermint Larry is out of town. Unfortunately, Captain K'nuckles starts to play tricks on Candy Wife, until he tells Flapjack he will marry Candy Wife.
Tired of Bubbie always questioning his authority, Captain K'nuckles decides to locate the ship where his Captain's papers are stored, and show them to Bubbie so that she will finally know that Captain K'nuckles is for real! But on the ship, Flapjack and Captain K'nuckles find out something neither of them ever expected, and they also find out that they might not be alone on this sunken ship! After K'nuckles bets Peppermint Larry that he could eat an entire jar of candy, and wins, one of the customers bet on Flapjack after he gets tired of hearing him say "adventure" when he comes in the Candy Barrel. If Flapjack loses the bet on capturing Eight-Armed Willy, Flapjack is forbidden to say the word "adventure" ever again.
When Bubbie gets a stomach ache, Flapjack must make the dangerous journey into her stomach to fix her. Mind the Store, Don't Look in the Drawer: Dr. Barber leaves Flapjack and K'nuckles to look after his shop, with one very important rule.
K'nuckles and Flapjack visit a storytelling club, where K'nuckles finds out that his own stories may be outdated. Flapjack tricks K'nuckles into believing that there is a sea monster attacking Stormalong.
Flapjack gets invited to a birthday party, but feel embarrassed when the other kids perceive K'nuckles and Bubbie as 'weirdos', including for himself. Flapjack pretends to be a dog for Lady Nicklebottoms while K'nuckles finds the actual dog. However, after Flapjack and Lady Nicklebottoms have such a good time together, Charles (Nicklebottoms' butler) gets jealous and attempts to throw Flapjack into the sea. Meanwhile, K'nuckles experiences the joys of owning a dog.
In the first half-hour long Christmas special, Flapjack celebrates "Low-Tides Day" and awaits his gifts from Poseidon, while K'nuckles tries to find a hidey hole from being sacked by mermen for being a bad kid.
Bubbie kicks K'nuckles out, and Flapjack tries to reconcile the two. When the fat police constable 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 offensives.
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 disliking 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 get stranded on a strange island and are unable to find the ocean.
K'nuckles and Peppermint Larry make a bet, and the winner receives a kiss from Candy Wife. K'nuckles' wish that everyone in Stormalong would disappear comes true, but soon begins to regret making his wish.
Flapjack enters the navy, only to find it's not exciting as he thought it was. K'nuckles becomes infested with termites.
Flapjack becomes upset when his picture appears in the paper. Flapjack tries to help Lolly Poopdeck get respect.
There are dire consequences when Flapjack impersonates a sailor.
When Peppermint Larry falls ill, Flapjack and K'nuckles are forced to go fishing for food. K'nuckles becomes the new mayor in Stormalong.
When K'nuckles continues to trick people and blame ghosts, Flapjack consults Jaude, 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 in order 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.
Flapjack and K’nuckles attempt to take advantage of weather-related panic. Flapjack and K'nuckles wreak havoc on a civilization in the clouds.
Flapjack tries to clear K'nuckles' name when he gets accused of stealing candy. Flapjack and K'nuckles consume a new drink at the Candy Barrel, but when they drink too much, it turns them into fish.
