|1a||WakDot||Brain invents a device that can conjoin people. He uses it on Wakko and Dot. ZakKo make their first appearance in this episode.|
|1b||Wakko's Hat||Slappy has to run an errand before she can take Skippy, Yakko, Wakko, ZakKo, and Dot to the waterpark. She has Buttons look after Skippy and the Warners. Unfortunately, a giant monster steals Wakko's hat. Buttons talks in this episode.|
|1c||The Blue Dot||A short story where Yakko is painting a wall blue, but accidentally spills the paint on Dot. This episode suggests that Dot wears a black shirt and is the first appearance of Pakko, Makko, and Jot.|
|2a||Invasion of the Brain Swappers||When Brain swaps the minds of Wakko, ZakKo, Pakko, Makko, Dot, and Jot, it's up to Yakko to figure out who's who and swap them back.|
|2b||The Separation of ZakKo||Set in a Wakko's Wish universe, ZakKo find out that Minerva Mink is selling wishing stones. They each buy one and use them to separate. They become conjoined again by the end of the episode.|
|2c||Yakko's World 2.0||Yakko sings the nations of the world again, only updated this time.|
|3a||Brainstem||Brain sings the parts of the brain to the tune of "Camptown Races." This episode was originally part of Pinky and the Brain.|
|3b||Little Red Riding Mindy||Mindy needs to take a pie to her grandma's house (with Buttons making sure she's safe). However, Mindy gets distracted by Slappy and Skippy, who end up leading her to her grandma's house! Walter Wolf also makes an appearance in this episode.|
|3c||Rita and the Three Warners||In their quest for a home, Rita and Runt come across the water tower where the Warners live. Rita checks the tower to see if anyone lives there. When Yakko, Wakko, and Dot return home, they find that having Rita there is a pleasant surprise! Unfortunately, Rita seems to be causing trouble, so Rita and Runt's search for a home continues.|
|4a||Kat the Cat: The Beginning||Makko Warner answers an email that asks him what a crazy cartoon made by him would look like. He comes up with Kat the Cat, who jumps off the page with her friends: Doug the Dog, Min the Mink, Shirley the Squirrel, Bonnie Rabbit, Drake the Duck, and Narf the Mouse (who only says his name).|
|4b||The Return of Baloney||Yakko, Wakko, and Dot find themselves on the set of Baloney and Kids again, and this time, ZakKo, Pakko, Makko, and Jot are with them. Yakko, Wakko, and Dot, having encountered Baloney before, are fine with him, but ZakKo, Pakko, Makko, and Jot are thinking otherwise.|
|4c||The Three Little Toons and the Big Bad ZakKo||A parody of The Three Little Pigs with Yakko, Wakko, and Dot substituting for the pigs and ZakKo as the wolf (well, a two-headed wolf).|
|5a||Kat the Cat: The Shoe||Yakko, Wakko, and Dot try to help Narf the Mouse find his missing shoe.|
|5b||AnimeNiacs||Yakko becomes king of Animenia when Baloney appears.|
|5c||I am the Very Model of a Cartoon Individual||Yakko sings the ending song of the canon episode "H.M.S. Yakko." It should be noted that it is re-animated for this episode. Baloney is shown instead of Captain Mel, and ZakKo, Pakko, Makko, and Jot appear.|
|6a||Wakko and the Fox||Yakko recites a poem about Wakko running from a fox.|
|6b||Yakko Jacks||A parody of Apple Jacks commercials.|
|6c||The Rule of Divisibility||Yakko sings the divisibility rules for the numbers 2 through 12 to the tune of the Mexican Hat Dance.|
|6d||Good Idea, Bad Idea: Chili Dog||
Good idea: Getting a chili dog at a restaurant.
Bad idea: Getting a chilly dog at a pet store.
|7a||Kat the Cat: The Calculator||Kat the Cat discovers a squirting calculator and asks Yakko, Wakko, and Dot what's up with it.|
|7b||All the Words in the English Language (Part 1)||A returning scene in which Yakko sings all the words in the English language to the tune of the Mexican Hat Dance.|
|7c||The Return of Hercule Yakko||When Skippy goes missing, it's up to Hercule Yakko to find him.|
|7d||All the Words in the English Language (Part 2)||See 7b for information.|
|7e||Pakko-Man||Pakko finds himself getting chased by Pinky, Brain, and 2 other mice. This is a parody of Pac-Man.|
|7f||All the Words in the English Language (Part 3)||See 7b for information.|
|7g||Good Idea, Bad Idea: Going Swimming||
Good idea: Going swimming in the summer.
Bad idea: Going swimming in the winter.
|8a||More Animaniacs Stew, Anyone?||The Warners are cooking up Animaniacs stew again.|
|8b||Jottie and the Brain||Brain, with Jot's help, tries to take over the world by means of a drink that makes whoever drinks it get bigger. This episode indicates that Brain is 3 inches tall.|
|8c||Dottie the Squirrel||A returning scene from the first Animaniacs Stew episode. Dot, in Slappy's place, throws a bomb at the camera.|
|8d||Mindy and Hobbes||Mindy chases a bouncy toy tiger, and ZakKo (in place of Buttons) have to rescue her. Buttons says this is his favorite episode.|
|8e||KatDoug||Yakko, Wakko, Slappy (in place of Dot), Kat the Cat, and Doug the Dog (the latter two in place of ZakKo) have to rescue Pinky from Rita.|
|8f||Runt and Buttons||Runt and Buttons (in place of Rita) are searching for a home, and find a home with Minerva Mink. Unfortunately, they are soon kicked out.|
|8g||Good Idea, Bad Idea: Ordering Pizza||
Good idea: Ordering a pizza.
Bad idea: Trying to order a pizza to march.
|9a||Seeing Red||A bull enters the studio and starts chasing the Warners.|
|9b||Class Antics||Plotz finds out about ZakKo, Pakko, Makko, and Jot, and sends them to the classroom with their cousins. Unfortunately, they drive Miss Flamiel crazy.|
|9c||Kat the Cat: The Twin||Kat the Cat and her twin sister Kate become joined together, and it's up to Yakko, Wakko, and Dot to separate them. First appearance of Kat's sisters: Kate, Katie, and Jessica.|
|10a||Buttons on the Beach||The Warners take Mindy and Buttons to the beach. This episode explains why Mindy calls her mother "Lady."|
|10b||Cheese Roll Call||Pinky sings about cheese. This episode was originally part of Pinky and the Brain.|
|10c||Hair Today, Gone Tomorrow||Hair restorer gets poured on Dr. Scratchansniff's head, restoring his hair. Unfortunately, he pulls it out again while he deals with ZakKo, Pakko, Makko, and Jot.|
|10d||Schnitzelbank 2.0||Yakko, Wakko, and Dot teach Schnitzelbank (which they still refer to as the "international friendship song") to their cousins. Kat the Cat, Doug the Dog, and Min the Mink appear in this episode.|
|11a||Kat the Cat: The Tower||Doug the Dog, Shirley the Squirrel, and Bonnie Rabbit are building a 500-foot-tall tower next to the swimming pool. Kat the Cat doesn't like this, and wants Yakko, Wakko, and Dot to make them stop.|
|11b||Conjoin the Warner Brothers||Yakko and Wakko become conjoined accidentally.||
|11c||The Kid in the Lid Returns||A sequel to "The Kid in the Lid" and a parody of The Cat in the Hat Comes Back.|
|12a||The Time Travel Contest||Animaniacs crosses over with The Time Machine in this special episode.|
|12b||When You're Traveling||Yakko sings about time. This is a returning skit.|
|13a||A Game of Cat and Mouse||Rita interrupts one of Brain's plans to take over the world.|
|13b||Pool Party||The Warners invite some characters to a pool party with help from the viewer. This is the first interactive episode of the series.|
|13c||Good Idea, Bad Idea: Three Strikes||
Good idea: Getting three strikes in bowling.
Bad idea: Getting three strikes in baseball.
|13d||All the Words in the English Language: Part 2½||Never-before-seen footage of Yakko at the S's as he tries to sing all the words in the English language.|
|14a||Mime Time: Anvil Dropping||The Mime drops an imaginary anvil, then a real one falls on him.|
|14b||Pain of Glass||Yakko, Wakko, and Dot have to carry a sheet of glass to the Warner Bros. studio while crossing busy streets.|
|14c||Slap Happy Slappy||Slappy is being chased by Doug the Dog while she tries to get some walnuts from his tree.|
|14d||The Warnerpuff Toons||Yakko, Wakko, and Dot star in a parody of The Powerpuff Girls, as superheroes with rock-paper-scissors themed powers. Pinky and the Brain also star in this episode. First appearance and only Season 1 appearance of Takko, Jakko, and Zot.|
|15||Toon Story||The Warners star in a parody of Toy Story. Baloney and Illogica Safe appear in this episode.|
|16||Email Day||The Warners check their emails. This episode parodies the Strong Bad Emails from Homestar Runner.|
|16a||Video Games||Yakko is asked what he and his siblings would be like in a video game.|
|16b||Fan Club||Wakko is asked if he and his siblings have a fan club.|
|16c||Educational Song||Dot is asked why she never did an educational song.|
|17a||There's Baloney in Our Slacks!||Baloney appears in the water tower, and the Warners cannot reach their anvil supply. The title is based on a line from the theme song.|
|17b||Good Idea, Bad Idea: Tossing a Salad||
Good idea: Tossing a salad.
Bad idea: Tossing a salad to the person next to you.
|17c||Kat the Cat: The Speck||Kat the Cat discovers a speck full of creatures called Whats, but the others do not believe her, except for Yakko, Wakko, and Dot. This is a parody of Horton Hears a Who!.|
|17d||Thy Dungeon-Warners||A parody of the Thy Dungeonman games from Homestar Runner.|
|18||A Wacky Adventure||The Warners follow Bugs Bunny through one of his tunnels and end up in Wackyland. Gogo Dodo stars in this episode.|
|19||Tiny, But Not Toony||Pinky and the Brain try to take over the world by removing the tooniness from cartoon characters, but the Warners are on to their plan. The title is based on the first four words of the Tiny Toons theme song. The episode itself is based on the Tiny Toons episode "Washingtoon."|
|20a||Dot the Macadamia Nut||A re-animated version of the canon episode of the same name. Now features the Kat Krew, the Siamese Quadruplets, and the Warner cousins, as well as Elmyra and Gogo Dodo.|
|20b||Return of the Boomerang||Wakko throws a boomerang and tries to find a way to pass the time as he waits for it.|
|20c||Davy Omelette||Chicken Boo poses as the great frontiersman Davy Omelette. This is a returning skit.|
|20d||10 Short Films About Wakko Warner||A returning skit where we see 10 short films about Wakko.|
|21a||Katie at the Bat||A parody of the poem "Casey at the Bat," starring Katie the Cat.|
|21b||Miniature Goof||The Warners go to a miniature golf course. The title is the same as the third segment of the Tiny Toons episode "The Wacko World of Sports."|
|21c||The Toonathlon!||The Warners have an Olympic-style competition.|
|22a||Jot-Star Warner!||Jot is a superhero whose name parodies Homestar Runner.|
|22b||The Monkey Song||This is a returning song from the canon of Animaniacs. Dr. Scratchansniff sings about the Warners.|
|22c||Home At Last||Rita and Runt find a home at last: with the Warners!|
|22d||The Animaniacs Suite: Part 2||To celebrate the season finale, the Warners present clips from the previous 21 episodes. It is a sequel to The Animaniacs Suite.|
|23a||Meet Sikko||The Warners are given a present from Lon Borax, the animator who created them. The present turns out to be Sikko. The Zarner siblings appear in this episode.|
|23b||Pakko's Project||In order to catch Coach Nurse, Pakko suggests digging a pit and filling it with water, with a trail of items leading to it. Unfortunately, the Zarner siblings had the same idea.|
|23c||Makko's Show||Makko hosts Let's Take a Deal, a parody of Let's Make a Deal. Guest appearances by Illogica Safe and the Siamese Quadruplets.|
|23d||Sikko's Plan||Sikko invites the Zarner siblings and Coach Nurse to a pool party. Guess who doesn't show up.|
|24a||The Warner Song||A parody of "Scales and Arpeggios" from The Aristocats.|
|24b||Jot's Chase||Jot plays tag with Coach Nurse.|
ZakKo create a transporter that they hope will transport Coach Nurse to the water tower.
|25||Wakko Takes the Challenge||Wakko competes on Take the Challenge!, a game show parodying Poptropica's Reality TV Island. First appearance of the Warnerpuff Sisters.|
|26a||Dot's Machine||Dot creates a machine so the second season can have a crossover episode. This episode crosses over with Homestar Runner.|
|26b||Yakko's Survey||Yakko wants Coach Nurse to take his survey. This is the season finale and Coach Nurse's first speaking appearance.|
Season 3 consists of entirely crossover episodes.
|27||Warners, Inc.||The Warners are working in a factory involving crossovers. When a cat enters the factory, Sekoila (who debuts in this episode) tries to take advantage of it. This episode is a parody of Monsters, Inc. The Warners sing a parody of the canon song "The Ballad of Magellan" in this episode.|
|28||Warners University||This episode is a parody of Monsters University and the first appearance of Wacka and Wakka MaRakka.|
|29a||How Lucky They Are||Makko recalls an incident that happened when the Warners were chasing Coach Nurse. The Cat in the Hat appears and tells the Warners how lucky they are that they're not in extremely unlucky situations. He does so by reciting Dr. Seuss's book Did I Ever Tell You How Lucky You Are? to them as they imagine themselves in the situations.|
|29b||Makko Rock||Makko falls down a Fraggle hole and tries to get back to the studio.|
|29c||Borfin Blues||When the Warners see the Cat in the Hat again, ZakKo find out about the Borfin's purpose and use it to separate. They become conjoined again by the end of the episode.|
|30a||Warners Over Yonder||Yakko, Wakko, and Dot discover a portal and meet Wander and Sylvia, helping them stop Dr. Screwball Jones.|
|30b||Jot Runner and Brain E. Coyote||
Brain tries to capture Jot to gain her speed. He is helped by Wile E. Coyote in addition to Pinky, but Road Runner is helping Jot by telling her some strategies to use.
Season 4 Edit
|31a||Arcade Game-y!||The Warners visit the arcade and try to beat the game Super Warner Bros. (a parody of Super Mario Bros.), but they keep on dying in certain points of their playtime.|
|31b||Calamity 'n' Beeper: Chamele-Coyote||Calamity tries to catch Beeper while wearing an ACME Chameleon Suit. First Calamity 'n' Beeper segment.|
|31c||Road Warners||Yakko, Wakko, Dot and Jot (labeled "Rapidus Warnericus") star in a Road Runner cartoon where they play the speedy bird, and Pakko (labeled "Famishus canis") is their coyote predator.|