War Against Fuse
In The Future, Flapjack and K'nuckles left Stormalong due to a fusion invasion along with Bubbie. Stormalong seemed to have collapsed showing that Fuse had managed to destroy Stormalong and all of its residents. They approached Orchid Bay which had been invaded too, so K'nuckles and Flapjack accidentally split up which makes K'nuckles either fallen or captured. Flapjack seems to have survived up until this point. He is at Birthday Bash celebrating with his friends.
He apparently separated with Captain K'nuckles to look for Bubbie after the rumored destruction of Stormalong. Flapjack seems unaware about the war and is only focused on finding K'nuckles and Bubbie. He also doesn't seem to notice the monsters.
A New World
He arrived alone to The Wilds looking for help to find Bubbie. He has stationed himself in Leakey Lake. Flapjack says that he misses K'nuckles and Bubbie, and that losing them makes it an adventure to find them.
Flapjack joined a bunch of our heroes to celebrate the Birthday Bash. He was located on top of the birthday cake.
Attack of the Mother Blowfish
According to the KND SKWID Squad, the Momma Blowfish lays its eggs on the shore of Candy Cove. However, Eddy discovered the eggs, thinking they were jawbreakers, stopping himself from eating one after he smelled it. Instead, Eddy snatched up several of the eggs and ran off. Later, the enraged Mother returned to the beach early, sending the SKWID squad into full crisis mode. Hoping to stop Momma Blowfish from rampaging through Townsville, the remaining eggs and the only hatched Blowfish were gathered before the mother, but four were missing, as Eddy sold the remaining eggs off as pearls for Mother's Day. The SKWID Agent at Peach Creek Commons tells the hero to report to the Candy Cove Agent, who after pressuring Eddy further, is told two eggs were sent to Flapjack at Leakey Lake. The hero then heads to Leakey Lake in search for Flapjack. Once he/she arrives, Flapjack says the eggs were for Bubbie, but he lost one egg looking for her in Acorn Flats. He gives you one, and upon finding the other, (which hatched), the SKWID call you and send you to the SKWID Agent stationed at Mount Blackhead.
Blood GnatsIt seems that when he and K'nuckles arrived in the FusionFall world, Blood Gnats hid in K'nuckles's head and flew off once they arrived. Flapjack asks the hero to help him stop the Blood Gnats before they make people fall in love. He sends the hero to find the Tiny Blood Gnat Queen first. Once the hero finds the Tiny Queen, Flapjack sends the hero to find the Bloated Blood Gnat Queen after hearing a few kids stating that they saw one in a big tree. The hero heads to Sector V and scales the tree house. When the hero finds the gnat, Mandark calls the player (via NanoCom) to tell them that some big heart thing (Lonely Blood Gnat Queen) is in his old lab. The hero heads to Genius Grove and enters Mandark's House. Once inside the hero searches rapidly for the Queen. Soon he/she finds the Queen next to the Terrafuser on top of the house. Flapjack then requests that the hero return to him, stating that he is getting ready to transport them back to Blood Island. Once returning to the hero, Flapjack thanks the hero for helping him, and gives him/her a Blood Gnat hat that he made out of small ones.
Looking For Bubbie
Flapjack once again request the heroes help in finding Bubbie. He assigns the hero to talk to to the sea creatures (Fusion Minions) to see if they saw Bubbie. The hero arrives at the waypoint, where Flapjack (via NanoCom) tells him/her to talk to the Creepy Clawdads (Note: You must fight them). After "talking" to the Creepy Clawdads, Flapjack states that they aren't nice at all. He seems to then think the Great Ironjaws are nicer, so he orders the hero to talk to them. The hero defeats 3 Great Ironjaws, Flapjack states that they aren't any better then the Creepy Clawdads. He then remembers what he heard someone say about seeing the Stormalong Wishing Well. He guesses that Bubbie is there wishing she could find him. The hero checks the well and confirms that it is the Stormalong Wishing Well. The hero finds a page of Bubbie's journal while investigating the well, The excited Flapjack requests that the hero return to him and give him the page of the journal. 
"X" Marks the Spots?
After receiving a page of Bubbie's journal, Flapjack explains that the page has three "X" marks on it, He begins to guess that on of the spots is where Bubbie is. He asks the hero for further help in his quest. The hero checks the first spot on the map, without success in finding Bubbie. Still optimistic, Flapjack orders the hero to check the next spot on the map. The hero checks the second spot on the map, but once again finds nothing. All that is found is Eggplants and a Chicken. After failing twice, Flapjack refuses to give up. He orders the hero to check in the last "X" on the journal page. The hero arrives at the third and last "X" spot, but like the last to time Bubbie is not there. Though, Flapjack spots an anchor from Stormalong. The hero must then clear out the local Spider Toads to get a closer look at the anchor. After defeating 5 Spider Toads, the hero gets a closer look at the anchor. After examining the anchor, Flapjack orders the hero to return to his position. Flapjack confesses that maybe drawing X's on a map doesn't mean that you'll find what you're looking for when you get there. He gives the hero his/her's reward and states that maybe the journal will give him another clue. 
Flapjack seems to have given DexLabs an item of his for Nano development. After doing so, his Nano can be seen in DexLabs in a incubation chamber along with Titan. The item that he gave the scientist company is currently unknown.
After the training courses, the recruit finally completes his/hers' training and thus, earning the title "Hero". On Mt. Neverest, many heroes come to congratulate the recruit. Flapjack is present at the event. He praises the hero. After the hero completes the 4 missions Computress gives him/her, the hero must leave Mt. Neverest on Lady Rainicorn to journey to Sector V, for the start of their quest.
Flapjack was added to gameplay on May 5, 2010 as a part of the Mother's Day event. He also offered 2 brand new mission as apart of his appearance. A Nano of him was found in the game's files back in 2009. His Nano was released in May 2011, along with Jake, and Johnny Test.
Flapjack appeared during the Valentines Day event (2019). He was found at Candy Cove on top of Bubbie, who has gotten sick. Unfortunately, they brought some Blood Gnats with them and the player had to help get rid of them.
Trying to Cure Bubbie
Flapjack moved to Leaky Lake as a permanent NPC in the March update. He was sent there by the SKWID Squad to find some items to cure Bubbie's tummy ache. The hero must help him find a Space Chicken egg, a fish in the Loch Mess and a Cogfish gear. The items actually turn out to be for the SKWID Squad's breakfast. Later, Flapjack says that there is one more item they need to cure Bubbie: a Gooby Trap. Flapjack doesn't know what that is, so he sends the player to the infected zone to retrieve it. The hero brings the Gooby Trap to Numbuh 20,001. He panics and initiates the "self destruct sequence." The player talks to Numbuh One and gets him to call off the self destruct sequence. The player and Flapjack discover that Fusion Flapjack had tampered with Stickybeard's message in a bottle and tricked Flapjack into getting a Gooby Trap. The player tracks him down to his lair in the Fissure and defeats him.
Return to Stormalong
In Patch 2.11, Flapjack, Bubbie, and the SKWID Squad were temporarily removed from the game, to return in a future update.
FusionFall Retro Expansion
On October 17th, it was announced in a blog post that his Nano will be added in an upcoming expansion.
- His Fusion is armed with an anchor and does not appear on the map.
- For some strange reason that has happened ever since the Null Void (A.K.A The Academy) was created, every mission given by him has his true character located at Mt. Neverest instead of Leakey Lake. Another example of this glitch is Grandpa Max.
- Freddy Fishlegs at Park & Flush said that Flapjack and K'nuckles split up to find Bubbie. But while Flapjack is at Leaky Lake, K'nuckle's whereabouts are unknown.
- Due to his naivete, Flapjack doesn't think the Fusions are bad.