Framed around an Aquabats concert (shot at the El Rey Theatre), the band presents 2 stories before an audience of fans.
The Aquabats! in... Tortilla Trouble!: In a live-action segment, The Aquabats are attacked by a giant tortilla monster. Tracking it down to a remote Mexican village where it has grown even larger after being exposed to random toxic waste, the band works together to blow it up and provide the village children with plenty of delicious chips and guacamole.
The Aquabats In... It's A Beautiful Under World: In an animated segment, The Aquabats attempt to bypass L.A. traffic by drilling underground in their BattleTram, only to find themselves in a lost underground where they're held captive by a sadistic unicorn. Guest starring Chris Phillips as the Narrator.
Commercials: The Aquabats! Hovercraft 4000; InstaBro: The Party Buddy™

While investigating a series of bizarre attacks on fast food restaurants, Crash is captured by the maniacal ManAnt, a half-man, half-ant creature who plans to siphon Crash's growth power to create an army of giant ants and take over the world. Meanwhile, skipping lunch as they attempt to find Crash, The Aquabats try not to let their hunger stand in the way of stopping ManAnt's scheme. Guest starring Mr. Lawrence as the voice of ManAnt, Art Mitchell as the body of ManAnt and Rip Taylor as Magic Genie.^[3]
A Cartoon!: When the Aquabats crash land on the surface of the moon, the MC Bat Commander is kidnapped by a telepathic alien named Moon Cheese, while the rest of the band come under attack by a swarm of space bees (the deadliest bees in space).
Lil' Bat: Lil' Bat Makes Breakfast!
Commercial: Harry Hider Pine Scented Hair Shield

When The Aquabats stumble upon a curiously large egg hidden deep in a forest, they decide to incubate it until it hatches, unaware of what danger lies within. Once the egg opens to reveal a mutated bird monster which proceeds to attack the band, Jimmy The Robot's maternal instincts kick in, rendering him too emotionally attached to the creature - which he has named "Jimmy Jr." - to destroy it and save his friends. Guest starring Mega64 (Derrick Acosta, Rocco Botte and Shawn Chatfield) as HandiGel actors (uncredited).
A Cartoon!: After fending off the space bees, the Aquabats go off in search of the Commander only to wind up in the clutches of Moon Cheese, who plans to steal the Commander's mind energy to power an Earth-destroying moon laser.
Lil' Bat: Lil' Bat Opens A Coconut!
Commercial: HandiGel Sanitary Gel

Tensions and egos rise among The Aquabats after EagleBones' showboating guitar solos disrupt one of the band's concerts, prompting him to leave the group and "go solo". However, when EagleBones' estranged evil brother EagleClaw appears to challenge his kin to a guitar showdown, EagleBones' hubris gets the better of him, and it takes a spiritual vision and the aide of an invisible eagle to help him learn the true meaning of teamwork. Guest starring Jon Heder as EagleClaw, Lou Diamond Phillips as the Spirit of the Sun and Warren Fitzgerald as Dumpster Diver.
A Cartoon!: After escaping from Moon Cheese and his Moon Shadow soldiers, The Aquabats wind up in a cavern where Jimmy is kidnapped by a gigantic moon octopus.
Lil' Bat: Lil' Bat Humiliates A Ghost!
Commercial: High Tides

Following a messy encounter with a gang of muck monsters at the city dump, The Aquabats head to their local laundromat to get their outfits cleaned. Unbeknownst to the band, the laundromat has been commandeered by the evil Dr. Eva Mudlark, a disgruntled scientist who creates monsters out of dirt and garbage, who seeks revenge against The Aquabats for killing her muck beasts. Guest starring Kate Towne as Dr. Eva Mudlark, Art Mitchell as Trusty Dusty, and Warren Fitzgerald as Hobo #1.
A Cartoon!: Finding a Victorian-era submarine on the Moon, The Aquabats give chase through a series of underground lakes in search of Jimmy, who awakens to find himself imprisoned in strange dungeon.
Lil' Bat: Lil' Bat humiliates a shark!
Commercial: Ring in a Can

During a leisurely night drive, The Aquabats save a group of partying beachgoers from a gang of laser-blasting mummies. Making a hasty retreat in their BattleTram, with the mummies in hot pursuit on motorcycles, the band continues the party on board, where Ricky falls smitten with a fellow party guest, unaware she's actually a 3-headed siren in disguise bent on destroying everyone in sight. Guest starring Janet Paraiso as Quera, Hera & Vera.
A Cartoon!: After engaging in a heated submarine battle with the Moon octopus, The Aquabats discover a hidden underwater city where Jimmy's being held.
Commercial: Tiny Burgers

Songs: "Lady In The Corner", "Isn't It Lovely?"
Song notes: Though not performed in the episode, "B.F.F.!" (from Hi-Five Soup!) is heard in the background of a party scene. In another party sequence, 2 non-Aquabats songs are played, "Beat Fishin'" and "Wednesday" (a parody of "Friday" by Rebecca Black).

While goofing around in a spooky cemetery, the MC Bat Commander discovers a delicious burrito sitting atop a gravestone and decides to take it with him, unwittingly inviting a ghost into the BattleTram determined to get it back. With The Aquabats frightened out of their wits, the band is stuck trying to find a way to banish the phantom before he causes any more damage. Guest starring Matt Chapman as Bob Higginsbottom.
A Cartoon!: As Jimmy contemplates how to escape from the Underwater King's dungeon, The Aquabats breach the underwater city's dome to bust him out, flooding the city in the process.
Lil' Bat: Lil' Bat Finds An Onion!
Commercial: Mummy Spray

After the BattleTram runs out of gas in the middle of the desert, The Aquabats stumble across a peculiar Old West-styled town hidden in the hills. Soon discovering the town is actually a realistic theme park whose visitors have been held captive by a malfunctioning robot gunslinger (an homage to the 1973 movie Westworld), the band tries to devise a plan to save everyone from his clutches, enlisting the help of a flying naked mole-rat monster along the way. Guest starring Paul Scheer as The Cowboy Android Sheriff.
A Cartoon: As the underwater city collapses around them, The Aquabats rescue Jimmy from the flood, only to realize that the water has short-circuited his hardware, paralyzing him.
Commercial: The Aquabats! Lil' Bat Video Player!

During a rousing round of golf, The Aquabats accidentally cross paths with the Überchaun, a malevolent blue leprechaun, who places a curse upon the band members. To avoid being cursed forever, The Aquabats are given 3 challenges to complete, squaring off against killer trees, a grass monster, two mean old ladies, and an army of hyperactive gophers. Guest starring Dana Michael Woods as the Überchaun.
A Cartoon!: Escaping from the moon just before it explodes, The Aquabats discover Jimmy is infested with alien parasites.
Lil' Bat: Lil' Bat Terrorizes Some Ants!
Commercial: Slushi

The Aquabats meet Pilgrim Boy, a fellow superhero and inexplicable Pilgrim who possesses the power to shapeshift into anything, despite causing him physical pain in the process. After the band pester Pilgrim Boy one too many times to change into various things for their amusement, he gets fed up and leaves The Aquabats to face a giant potato bug attacking the Detroit pineapple plantation by themselves. Guest starring Samm Levine as Pilgrim Boy and "Weird Al" Yankovic as President Stuntcastin.
A Cartoon!: In an attempt to rid Jimmy of his brain parasites, The Aquabats shrink down to size and venture inside his body to reboot his system. Meanwhile, the BattleTram is attacked by a vicious space worm.
Lil' Bat: Lil' Bat Jumiliates A Fly!
Commercial: Snakey Snacks

Exhausted after a playing a rock concert, The Aquabats pull into an isolated truck stop to catch some sleep. Their peace and quiet is short-lived, however, when the mythical Floating Eye Of Death invades their rest area, transforming its inhabitants into mindless zombie drones. Holing up in the convenience store, The Aquabats must find a way to defeat the floating menace before they too start falling victim to its soul-stealing powers. Guest starring Becca Greene as Tina.
A Cartoon!: As Jimmy's anti-virus software kicks in and eradicates his brain parasites, The Aquabats race to escape from Jimmy's body before they too are destroyed.
Commercial: Stooped Fone!

Songs: "The Shark Fighter!" (From Hi-Five Soup!), "Feel My Steel"

When a strange meteorite crashes in the desert, The Aquabats arrive at the scene hoping to sell it for some quick cash, only to find it possesses dangerous otherworldly powers. With The MC Bat Commander horribly mutated from its effects, the band must find a way to not only restore their leader to his former self but also rescue a nearby woman from the clutches of a crazy cactus monster brought to life by the meteorite's same powers. Guest starring Paul Rust as Ronmark, Kate Freund as Zalga and Finau Tafua as the Cactus Monster.
A Cartoon!: After escaping from Jimmy's body and successfully dodging the space worm, The Aquabats set a course for a strange nearby planet to repair the BattleTram.
Commercial: S.C.A.B.S.

In the midst of traveling on a world tour, The Aquabats are lured into a shady roadside sideshow advertising a "real-life CobraMan", only to end up having the BattleTram stolen by a wrestling mask-wearing carnival barker named Carl (modeled after co-director/performer Chapman's Strong Bad character). Facing certain unemployment without transportation, the band must challenge Carl to an all-or-nothing duel with his CobraMan monster to reclaim their vehicle, or else they'll have to return to their day jobs. Guest starring Matt Chapman as Carl, Bailee Madison as Scruffy Scruff actress and Brad Davis as the voice of CobraMan.
A Cartoon!: When the Battletram lands on a planet inhabited by friendly barbarians (the Gnarbarians), The Aquabats try to find a way back home with the aid of a magic dagger.
Commercial: Scruffy Scruff

Down on their luck and out of money, The Aquabats try to find an opportunity to re-establish their superhero status in order to help sell their surplus of merchandise. When an impending alien invasion masterminded by the diabolical Space Monster "M" defeats the city's other, far more competent superhero teams, it's up to The Aquabats alone to summon their collective strengths and stop him before he destroys the planet. Guest starring "Weird Al" Yankovic as SuperMagic PowerMan!, Stephanie Allynne as Lanolin Lady!, and Dallas McLaughlin as Space Monster "M". Former Aquabats members Corey Pollock and Boyd Terry appear as fellow superheroes Chainsaw and Catboy, their respective Aquabats stage names.
A Cartoon!: Using the magic dagger to repair the BattleTram, The Aquabats fly into space where they meet The Time Sprinkler, who throws the band into a time loop repeating the last year of their lives, effectively sending them back to the series' first episode.
Commercial: Poppin' Shocker! Electrode Suit

Songs: "It's Showtime!", "We Don't Stop" (reprise)

Following their previous encounter with Space Monster M, The Aquabats crash-land back on Earth, awakening to realize they have no memory of what happened or who they are. Hailed as heroes by the adoring public, the band starts slowly piecing together their identities. After managing to destroy a rampaging mutated Ronmark (from the episode "Night of the Cactus!"), the band find themselves overwhelmed with demands from citizens seeking their help. Guest starring Tony Hawk as Journalist #1, Eric Koston as Journalist #2 and Paul Rust as the Voice of Ronmark.
Animated Segment: EagleBones explains in an animated flashback how he came to join The Aquabats, meeting the band in a desert roadhouse during an nomadicy journey. This segment is animated in a rotoscoping technique inspired by the 1981 film Heavy Metal.
Lil' Bat: Lil' Bat Has A Dream!
Commercial: Sonic Boom 3000

Songs: "Help Me!"

While returning home from a relaxing ski vacation, The Aquabats get trapped in a snow embankment and are forced to spend the night without power in the BattleTram. In an overt parody of the 1982 film The Thing, a malicious shape shifting alien sneaks aboard the vehicle after disposing of Jimmy to assume his form and enacts a scheme to turn the Battle Wagon into a rocket to return to his galaxy while having the human Aquabat members turned into rocket fuel. Successfully evading capture, Crash must learn to overcome his fears and rescue his pals from certain doom.
Animated Segment: Crash remembers how he met the other The Aquabats "on his first day of public school" (quoting the band's 2000 song "Pizza Day!"). This segment was animated by Shmorky of the humor website Something Awful.
A Cartoon!: Lil' Bat Drinks A Soda Pop!
Commercial: Meal-A-Rang

Songs: "I'm A Bad Thingy!"

After a giant mutant "flea beetle" attacks a local supermarket, The Aquabats trace it to a nearby farm growing genetically enlarged produce, which happens to be run by Jimmy the Robot's estranged parents. Tensions rise between Jimmy and his eccentric scientist father over Jimmy having abandoned his farm life, but when a gigantic mutant worm swallows Jimmy's mother, the 2 must work together to rescue her. Guest starring Mark Mothersbaugh and J.J. Neward as Jimmy's parents, Ralph and Martha Goodman.
Animated Segment: Jimmy explains his version of how he joined The Aquabats, answering a newspaper ad for a band seeking a saxophone-playing robot. This segment utilizes an early computer animation style reminiscent of the Dire Straits' "Money For Nothing" music video.
A Cartoon!: Lil' Bat plays tennis!
Commercial: Dirt Clod

The Aquabats spend the summer participating at Camp RadVentures, a summer camp where kids are trained in The Aquabats' superpowers to become AquaCadets. When a group of campers are kidnapped in the middle of the night, the band realizes it's the work of a mythical shapeshifting beast, and the Commander's suspicions quickly fall upon the camp's beloved and irrepressibly perky counselor Jewel. Guest starring Leslie Hall as Camp Counselor Jewel.
Animated Segment: The MC Bat Commander tells about The Aquabats' origins, recounting the band's original Aquabania mythos while quoting from their 1997 song "Theme Song!". This segment is animated in the same Anime style of the 1st season's cartoons.
A Cartoon!: Lil' Bat Uses A Microwave!
Commercial: Captain Turnip's Grocery Island

Songs: "Summa Camp!", "The AquaCadet Anthem!"

When The Aquabats act as judges for a local Battle of the Bands contest, Ricky falls in love with one of the performers, mediocre folk singer Rachel Moonbug, rigging the vote in her favor and infuriating the other contestants, death metal band Asthma and dubstep artist Skillsawz. Sensing their desire for revenge, the nefarious Silver Skull bestows Asthma and Skillsawz with his dark powers, transforming them into "The AntiBats" and sending them forth to destroy The Aquabats. Meanwhile, Ricky quits the band to run off with Rachel Moonbug, but as the Silver Skull and The AntiBats close in on The Aquabats, he must make a choice between true love and saving his friends. Guest starring Mark Fordham as Silver Skull, Mikey Way as Asthma Lead Singer, Noël Wells as Rachel Moonbug and Martin Starr as Shred Center MC
Animated Segment : Ricky remembers how he came to join The Aquabats, recalling his early life in the dance crews on the streets of Hi-Five City. This segment utilizes stop motion animation.
A Cartoon!: Lil' Bat Goes To The Dentist!
Commercial: Popcorn Pants

After getting lost on their way to a Christmas tree lighting ceremony, The Aquabats arrive in a remote village ruled by the tyrannical Krampus, a demonic beast-like creature who has outlawed all mention and celebration of Christmas under penalty of severe lashings with a switch. The overly-festive Aquabats are promptly captured and incarcerated by the townsfolk, and their only hope for rescue lies with the big man himself, Santa Claus. Guest starring Robert Smigel as the voice of the Krampus, Matt Walsh as Santa Claus and Jordan Burt as Marco.
A Cartoon!: Lil' Bat Goes Caroling!
Commercial: Christmas Tree Man

When a gang of vicious mutant land sharks emerge from the sea to wreak havoc on land, The Aquabats join forces with the legendary Shark Fighter, a wavy-haired ocean vigilante on a self-imposed quest to fight sharks. Impressed by his potential, the Shark Fighter takes Crash under his wing to teach him the art of shark fighting, but Crash may just see more in the Shark Fighter as the big brother he's always wanted. Guest starring Rhys Darby as The Shark Fighter.
A Cartoon!: Lil' Bat Grows A Plant!
Commercial: Little Brother

When the city's cutest kittens start being abducted by gigantic teleporting cat men, The Aquabats trace it back to Kitty Litter, a ferocious feline using unwilling kittens to power a gigantic cat robot as part of a scheme to cover the planet with garbage. When most of the band are kidnapped by Kitty Litter, it's up to Crash to get over his pet dander allergies and save the world from becoming a global trash heap. Guest starring Ben Garant as the voice of Kitty Litter and Julia Prescott as Gina.
A Cartoon!: Lil' Bat Raises A Fish!
Commercial: Skeletiger