Codename: Kids Next Door had plenty of sequel episodes over its run, they may have well been Story Arcs.
- "Operation: C.A.K.E.D." (which were all named with a number at the end, save S.I.X.) dealt with the K.N.D confronting the Delightful Children for refusing to share their birthday cake and trying to either take it away from them, make sure other kids got a taste of it or both, only failing in the the sixth one due to some clever manipulation by the Delightful Children. Likewise the final episode, Operation: I.N.T.E.R.V.I.E.W.S., was centered around this.
- "Operation: C.A.B.L.E.-T.V." led into "Operation: G.R.O.W.-U.P.", where the Delightful Children found the Age-Changing Cigar previously owned by Mr. B to turn the entire world into babies and used it to turn Numbuh One into an adult, then his teammates need to recover the cigar to get their old leader back.
- "Operation: S.P.A.N.K." leads up to "Operation: L.O.C.K.D.O.W.N.", detailing how the kids tricked Count Spankulot into spanking an innocent child, later, the judge who put him away, and sent him to a normal prison instead of theirs. Out of revenge, Count Spankulot spanked Numbuh One without his gloves to transform him into a Spank-Happy Vampire after luring him into his cell with his hypnotic abilities, while the others wildly assumed he escaped from prison, at which point Numbuh One would do the same to his teammates and Numbuh Three's Big Bottom Rainbow Monkey Doll after ordering a lockdown of the treehouse.
- "Operation: S.U.P.P.O.R.T.", "Operation: K.I.S.S.", "Operation: S.P.A.C.E." and "Operation: E.N.D.." centers on Numbuh Five's older sister, Cree, formerly Kids Next Door operative Numbuh 11, and now, a Teen Ninja siding with the evil adults, trying to destroy the Kids Next Door Moonbase by making it collide with the sun. Chad/Numbuh 274 already tried Cree's plan after Numbuh One found out his 13th Birthday was approaching and he tried to avoid being decommissioned at all costs, such as making sure those invited to his party, including the Sector V team, didn't learn the truth by raising their ages and getting them wrongly decommissioned. However, this plan fails. He tells Cree he failed when she finally arrives in the garbage pod Numbuh Five previously launched her out of, at which point he joins her.Cree: (arriving at the Moonbase in the trash chute she piloted, which was previously launched out of a KND spacecraft in an earlier episode by Numbuh Five) Crud! Time for Plan "B".
Chad: Think you could use some help?
Cree: Sure, kid, come on.
Chad: I'm not a kid! I'm a teenager! (hops into the trash chute with Cree and escapes the Moonbase) - "Operation: B.E.A.C.H." and "Operation: K.A.S.T.L.E." detailed King Sandy's attempts to marry Numbuh Three, only to later fall in love with her younger sister, Mushi.
- "Operation: C.L.U.E.S." and "Operation: S.P.A.N.K.E.N.S.T.I.N.E." served as the sequels for the King Sandy episodes, wherein as Mushi and Sandy's relationship had developed over time, it caused her to develop his disdain for Rainbow Monkeys. During a dinner party at the Gilligan Residence, Mushi is Grounded Forever for "murdering" her sister's Posh Party Rainbow Monkey doll thanks to Numbuh Two's detective skills. Later, Mushi steals Count Spankulot's powers and brings the Rainbow Monkey back to life as a spank-happy monster as revenge, only for her grounding to be increased to five life sentences and later to run away from home.
- "Operation: E.N.D.", "Operation: T.R.A.I.N.I.N.G.", "Operation: S.L.U.M.B.E.R." and "Operation: G.R.A.D.U.A.T.E.S." focused on two topics: Numbuh 2's younger brother, Tommy, training to be a Kids Next Door operative and the theft and recovery of the Kids Next Door Code Module. The Code Module is needed to induct new Kids Next Door operatives by inserting samples of their DNA after graduation, specifically, boogers, and Father needed it to power a machine that turns Kids Next Door operatives into animals. After Father failed to steal the Code Module himself at the Arctic Base while Tommy was in the middle of his training, it was later stolen at the Moonbase by the Teen Ninjas, plus, another traitorous Kids Next Door operative whose 13th birthday was approaching who was invited to Numbuh 86's slumber party, until the Sector V team recovered it just in time for Tommy's graduation (especially with the computer game that served as the prequel to the episode). Tommy had no choice but to resign from the Kids Next Door to avoid being hit by the device, then turned said device against Father and the Delightful Children by stealing their DNA and inserting them into the Code Module, allowing him to destroy said device afterwards, at which point he later became "The Tommy".
- "Operation: I.T." serves as the sequel to "Operation: G.R.A.D.U.A.T.E.S.", where Father and the Delightful Children from Down the Lane are still in the Kids Next Door database after Tommy stole their DNA to turn their animal transforming device from the earlier episode against them shortly after his resignation. They were still in the database in a game of tag and the winner would become the new KND Soopreme Leader with Numbuh 362, unable to handle the pressure, considering handing over the job to someone else. Father planned to infest every treehouse with broccoli until Numbuh 362 used it against him, with a little help from the Delightful Children, because not even they like broccoli. After the fact, Father's and the Delightful Children's DNA are removed from the Code Module and Numbuh 362 retakes her role.
- "Operation: J.E.W.E.L.S.", "Operation: R.A.B.B.I.T.", "Operation: C.H.O.C.O.L.A.T.E.", "Operation: L.I.C.O.R.I.C.E." and "Operation: C.A.R.A.M.E.L." detailed the story around Numbuh Five and her arch-rival, Heinrich Von Marzipan.
- "Operation: P.R.E.S.I.D.E.N.T." and "Operation: S.N.O.W.I.N.G." set up "Operation: E.L.E.C.T.I.O.N.S.", detailing the fiasco with the school president and the consequences that followed.
- "Operation: H.O.U.N.D." set up "Operation: D.O.G.H.O.U.S.E.", which involved homework-eating weredogs.
- "Operation: M.A.U.R.I.C.E." lead into "Operation: T.R.E.A.T.Y.", regarding the existence of undercover Teen KND Operatives.
- "Operation: W.H.I.T.E.H.O.U.S.E.", "Operation: G.I.R.L.F.R.I.E.N.D.", and "Operation: T.R.E.A.T.Y." cover the mysterious overseers, later revealed to be Numbuh Infinity and Numbuh 74.239, who have been secretly watching and testing Numbuh One all throughout the season. Meanwhile, "Operation: M.E.S.S.A.G.E.", "Operation: S.C.I.E.N.C.E." and "Operation: A.M.I.S.H." discuss the rumored Splinter Cell, a traitorous faction in the Kids Next Door that wants to eradicate all adults and teenagers from the planet. Both of these storylines ultimately collide in Operation: I.N.T.E.R.V.I.E.W.S., where it's revealed that the Splinter Cell never existed, as it was a way of covering the tracks of the Galactic Kids Next Door, which Numbuh One has been chosen to join as its very first Earth Operative.
- "Operation: C.H.A.D.", "Operation: E.N.D.", and "Operation: T.R.E.A.T.Y." are the three Chad-centric episodes which cover the relationship between Nigel and Chad, starting with Chad's introduction as The Ace of the KND and Nigel's idolization of him, Chad's betrayal and fall from grace, and the moment Nigel finally surpasses Chad and cements his place as the best Kids Next Door operative on Earth.
