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 refuses to give Flapjack and K'nuckles any candy unless they bring him candy wrappers to exchange for the treats. Selfishly, K'nuckles takes all of the candy for himself, breaking Flapjack's heart. He discovers Larry's true plans when trying to exchange more wrappers; the wrappers formed a map when put together leading to Candied Island. K'nuckles tries his best to regain Flapjack's friendship. He does this, but Flapjack destroys the wrapper that Peppermint Larry needed to get to Candied Island. Once K'nuckles explains all this, they forge the wrapper and trade it in. Peppermint Larry then attempts to use the map to get to Candied Island, but instead it leads to Pickled Island. He is still happy that he has his candy-wife with him; however, this changes when he sees her having an affair with a giant pickle.
K'nuckles locates a map that supposedly leads to Candied Island, but when Flapjack goes "blind" due to his long hair covering his eyes (developing superhuman hearing and seeming telepathy in the process to compensate), a group of barbers steal the map. Flapjack and K'nuckles chase after the barbers in hopes of regaining the map, which turns out to not be a true map at all, but a goofy note Flapjack wrote to K'nuckles about their friendship.
Flapjack wants to know what Bubbie does throughout the day, so he tries to figure it out.
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. However, it is inhabited by a terrible beast named Cammie. K'nuckles attempts to build a raft in hopes of escape, while Flapjack befriends the monster and helps her get some food. K'nuckles attempts to build a raft three times; one out of sardines, which is stolen and eaten by a great white shark, one out of bananas, which is stolen and eaten by an "undersea gorilla", and one made out of wood, which Flapjack pointed out would not float. Eventually, Cammie simply gives them a new boat for them to get back to Stormalong.
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.
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 real right hand, and willingly returns K'nuckles's hand. Unfortunately, thanks to Flapjack's big mouth, K'nuckles's body is now only composed of two eyeballs and a wooden right hand.
To celebrate Flapjack's birthday, Captain K'nuckles and Flapjack sail westward, as forced by Bubbie in search of Candied Island. Flapjack is oblivious to the danger around him, despite scenery such as burning ships, monsters, crazy old hermits, and other such hazards. The mere mention of the word "West" causes monsters to appear, and the entire direction is shrouded in a "curse". After hours of traveling west Bubbie and K'nuckles declare that there is nothing in the west and try to go home. However, Flapjack builds a raft to keep sailing west, taking K'nuckles along for the ride. K'nuckles and Flapjack go crazy after drinking seawater, suffering hallucinations, but Bubbie rescues them. At the end, Bubbie gives Flapjack a "W" for his compass, but K'nuckles sold the compass for maple syrup. K'nuckles uses the "W" as a bottle opener and throws it into the ocean.
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. It turns out that K'nuckles II has the apparently supernatural ability to infect anybody who is cruel to Flapjack with the plague by flicking its fleas on them, and, almost overnight, everybody in Stormalong but Bubbie and Flapjack himself are infected (although the original K'nuckles purposely gets infected to avoid helping Doctor Barber take care of the others). Flapjack has no choice but to send his rat friend to "Plague Island". Then it turns out that Flapjack's blood carries a natural antibody to the plague, and he is the key to the survival of the denizens of Stormalong, which explains why K'nuckles and the other infected inhabitants of Stormalong claim that they "cannot live without him". The episode ends as an infected Dr. Barber appears with a large hypodermic needle to get a blood sample from Flapjack.
Flapjack, Captain K'nuckles, and Bubbie journey to the Bottom of the World to retrieve K'nuckles' lost "sittin' muscle" (his bottom), which he replaced with a wooden belt. They go to the peak of a mountain, where his sitting muscle is located. Flapjack and K'nuckles find his sitting muscle frozen in ice, and are unable to get it out. Upset that he might freeze to death, K'nuckles gets depressed. Flapjack tries to make K'nuckles feel better by hugging him, but the heat from his hug makes K'nuckles' sitting muscle thaw out. K'nuckles puts on his sitting muscle and Flapjack and K'nuckles slide down the mountain. But the friction from the slide causes K'nuckles' sitting muscle to be burned off, and Flapjack and K'nuckles are frozen in ice.
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. They go to the Knot Festival to try to find a cure for his curse. They go around trying to find cures, until K'nuckles hears Flapjack speak. K'nuckles becomes angry when he realized that Flapjack had the ability to speak all along, merely faking it so K'nuckles would take him to the Knot Festival. K'nuckles asks Flapjack to cover his ears while he uses "strong language", which earns him a trophy. Flapjack finds a Singing Booth, and starts singing songs. He sings for so long that he eventually truly loses his voice. When they return, K'nuckles exposes Flapjack's lie to Bubbie, though she doesn't believe him, and he gets brutally stung by a large group of jellyfish that she had recently swallowed.
After an incident with some women at the Candy Barrel, Captain K'nuckles tells Flapjack about when he was at a party, and everyone had dates, except for K'nuckles, whose date ditched him. He has had Misogyny ever since. When Bubbie suggests for K'nuckles to get a girlfriend, K'nuckles is reluctant to get one, until he sees a wig and his reflection at the wig store and falls in love with it. K'nuckles and the wig (his reflection in a mirror) go on a date, and eventually decide to get married.
Peppermint Larry hosts his annual Adventure Beard-Off. Men with fantastic beards compete to win Peppermint Larry's candy-daughter's hand in marriage. Captain K'nuckles wants a beard to compete (he and Flapjack think that the daughter is made of candy, and they both want to eat her), and Flapjack makes a fake beard out of hair and glue. The next morning, K'nuckles wakes up with a beard and enters the competition. Then, he discovers that his "beard" is actually Flapjack stuck to his face and covered in hair and glue. After failing all three rounds of the competition miserably, Flapjack jumps off K'nuckles' face and starts dancing, much to the enjoyment of the crowd. Then, the hair and glue fall off of Flapjack, and it is revealed that his beard is fake. When asked to quickly pick a winner, Peppermint Larry chooses The Dock Hag with a beard. It is then discovered that Peppermint Larry's daughter is not as beautiful as expected (or made of candy), as she is adopted.
Peppermint Larry is preparing for the Stormalong Pun-Off, where he will compete with comedy legend, Punsie McKale, in joke-telling. To practice, Peppermint Larry teaches Flapjack puns, as Flapjack is a very bad joke-teller. On the day of the Pun-Off, Peppermint Larry starts getting nervous and puts on a very bad show, and Punsie McKale clearly puts on a better show. K'nuckles then gets bored with their jokes and tells some jokes of his own. K'nuckes is so well-received by the audience, that the audience goes wild with laughter and sink Stormalong Harbor. In the end, Peppermint Larry and Punsie McKale are shown sailing on the sea inside a giant mug of root beer because, according to Peppermint Larry's joke, "Root beer floats!"
Stormalong is visited by an eccentric man promising wonders never seen before. The "wonder" turns out to be a film. The film shown is just the man walking on a sidewalk, and sitting in a chair. This bores Flapjack, but the other denizens of Stormalong are entranced by the film. Flapjack is left to entertain himself. He chooses to balance himself on a floating piece of driftwood. The "cinematographist" sees him and records Flapjack's balancing act. K'nuckles sees Flapjack as a celebrity after seeing him in the new movie. He asks Flapjack if he can get K'nuckles to appear in a new movie. Flapjack agrees, on the condition that K'nuckles stay out of the theater, and takes him on an adventure. The newest movie turns out to be Captain K'nuckles repetitively falling off a board. This annoys K'nuckles, who saw the movie through the window of the theater (Not technically in the theater, keeping the promise he made). However, Flapjack is thoroughly amused, and the episode ends with him rolling on the floor laughing.
While searching for Candied Island, K'nuckles and Flapjack find an island with a mechanical genie. The genie tricks Flapjack and K'nuckles into thinking it knows where Candied Island is, and K'nuckles bets their lives on a game where he must find a ball under one of three cups. K'nuckles loses, and he and Flapjack become the genie's butlers forever. After making them do pointless tasks, K'nuckles is infuriated with the genie and tries to destroy it. Flapjack and K'nuckles then discover that the mechanical genie was actually a game controlled by a giant baby that keeps them on the island as his 'toys'. The island is then shown to be the ball under the mechanical genie's cups, who is back at Stormalong. Flapjack then pulls the genie's electric cord from an outlet.
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. Instead, he ends up helping people, such as shooting an old man with a cannon and fixing his back instead, and smashing a replica of Candied Island Peppermint Larry made over seven years, but making a candy thief trip and fall into the ocean. After Flapjack gives up and walks back to K'nuckles, he finds out that a bunch of ugly sailors on a ship he and K'nuckles were swabbing at the beginning of the episode are angry with Flapjack because they can see their hideous reflections on the floor. When Flapjack tells the sailors that K'nuckles told him to swab it, they beat K'nuckles up.
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.
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.
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.
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.
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.
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.
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.
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.
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.
