In "Operation: RABBIT (Rescue Aids Beloved Bunny In Trouble)", Numbuhs 2 and 5 must rescue the first grade class's pet rabbit before it is turned into a chocolate bunny by Heinrich Von Marzipan. In "Operation: FLUSH (Foolish Loser Undoes Sinister Hope)", the villains attempt to capture the KND Treehouse, but the Toilenator, trying to be helpful, only hinders their plans.

In "Operation: F.O.O.D.F.I.T.E. (Fiendish Old Ogre's Disgusting Food Is Thrown Everywhere)", the KND are dismayed to discover that Grandma Stuffum is the new cafeteria lunch lady and she's got some pretty nasty recipes to foist on her pint-sized nemeses. In "Operation: C.L.U.E.S. (Cutlery's Location Uncovers Elementary Solution)", a dinner get-together between Numbuh 2 and Numbuh 3's respective families turns sour when Numbuh 3's Posh Party Rainbow Monkey doll is badly damaged with a fork in its back. Now it's up to Numbuh 2 to figure out the murderer of the doll.

In "Operation: N.U.G.G.E.T. (Numbuh Uncovers Golden Glistening Edible Treat)", Numbuh 4 discovers a chicken nugget that initiates a chicken nugget rush. In "Operation: M.A.C.A.R.R.O.N.I. (Museum's Artwork Cruelly And Recklessly Ripped Off Nearly Impossibly)", the Kids Next Door have the misfortune of swapping the Toilenator to Mr. Boss with the unlucky Numbuh 13, who informs the operatives of the adult villains' plans for a macaroni dinner by ransacking a museum of macaroni art.

In "Operation: P.O.O.L. (Prevent Opposite Operative's Larceny)", Numbuh 4's newly-installed backyard pool is the portal into an alternate dimension where everything is the opposite of everything in the real world.

In "Operation: C.A.K.E.D.-F.O.U.R. (Children's Annual Kompetition Exposes Devilishly Fiendish Operation Up River)", the Delightful Children From Down the Lane decide to give their birthday cake to the winner of the annual Tubathon race and everyone is eager to go for it. No one is more eager than Numbuh 2, who plans to use his old tube, Betsy, and "farfegtubing". But are the Delightfuls keeping their word about the cake or are they luring the competitors into a trap?

In "Operation: S.I.T.T.E.R. (Sweetheart's Involvement Transforms The Evening's Reality)", the brothers Gilligan have gotten a new babysitter: the villainous Cree Lincoln! For Numbuh 2, this will either be a dream come true or a nightmare. In "Operation: S.A.T.U.R.N. (Stuff Abducted Turns Up Revolving Nowhere)", everyone's collections of Rainbow Monkey toys are mysteriously vanishing. The KND investigate and discover the toys revolving around the planet Saturn as its big ring!

In "Operation: C.H.O.C.O.L.A.T.E. (Chocolate Hunter Operative's Chocolatized Opponent Literally A Touchy Enemy)", Numbuh 5 goes to the planet Mars to pick up some marshmallows as part of dessert with her family after dinner. But upon her return, she discovers her family and friends are being menaced by an old foe who now is a mere shell of his old self. In "Operation: M.A.T.A.D.O.R. (Misbehaving Agent Teases Adults During Organized Recreation)", Numbuh 4 is forced to choose between helping the KND battle the villainous Soccer Mom or engaging at his new gig as a ...

In "Operation: L.U.N.C.H. (Lizzie Underappreciates Nigel's Chowtime Hardworkingness)", Lizzie had made a romantic lunch for both her and "Nigie", but it gets stolen by Robin Food and his Hungry Men, who rob from the young and give to the old. In "Operation: M.U.N.C.H.I.E.S. (Morning Uncovers Needed Crunchiness Hiding In Enemy Store)", the KND discover that they're out of Rainbow Munchies cereal, so they try to go to a grocery store to get some more. But the only grocery store that sells such a product is the villains-only store called the Super-Villains Supermarket & ...

In "Operation: K.N.O.T. (Kids Necks Overwhelmingly Tied)", Numbuh 1, both literally and figuratively, risks his neck when he sides with an adult to rid children of snake-like ties. In "Operation: C.L.O.S.E.T. (Child Lost On Severely Elevated Tundra)", a boy gets lost in a closet and the KND are on the job in no time.

In "Operation: S.N.O.W.I.N.G. (Sickly Nigel Opposes Warped Incumbent's Nasty Grasp)", Numbuh 1 is sick in bed with a cold on a snow day. Even worse, the villainous Fourth Grade President is determined to bring the children, who are all taking advantage of the snow day, to school for a special assembly.

In "Operation: M.A.U.R.I.C.E. (Mature Agent Undergoes Reprogramming Into Childhood's Enemy)", an operate named Maurice is decommissioned from the Kids Next Door after he attains the age of 13. He has been working on a cure for chicken pox. The one who is saddened the most by his departure is Numbuh 5, so she suggests that they keep an eye on him so that the teenagers don't recruit him.

In "Operation: L.O.V.E. (Little Operative Very Emotional)", Numbuh 3 stars as the lead female in a "West Side Story"-style romantic musical. But when Numbuh 4 interrupts the play, the war that follows between the Kids Next Door and the Delightful Children From Down the Lane is anything but staged. In "Operation: C.O.U.C.H. (Creepy Otherworld Under Cushiony Heap)", Numbuhs 1, 2 and 5 all go off to China after Numbuh 4 falsely alerts them of trouble there. He then watches TV in their absence, but Numbuh 3 doesn't leave, either, and they fight over the remote control, ...

In "Operation: D.O.D.G.E.B.A.L.L. (Dangerous Old Dude's Game Excellently Beats All Little Losers)", the powerful Dodgeball Wizard believes that adults are better at playing dodgeball than kids, so when he learns of "the one called Beetles," a kid who is a greater dodgeball player than he is, he becomes determined to destroy his rival. And that rival is, apparently, Numbuh 4! In "Operation: F.E.R.A.L. (Friends Extract Really Ape-ified Leader)", Numbuh 1 is sent to retrieve an important code from Rainbow Monkey Island, but after a run-in with the Delightful Children ...