| ShortSummary | - During the New Year period, The Loonatics face off against Boötes Belinda, a villain and his band who uses rock music to terrorize Acmetropolis. When Zadavia is captured, he orders Tech to build a high-tech guitar for him. Now the Loonatics must save Zadavia and defeat this evil band. It turns out that the band are robots led by Rupes Oberon, a man who wrote a national anthem for Zadavia on Freleng, but was shot down since there already was a national anthem: that had words. He uses the guitar to steal all of Zadavia's powers.
- Lexi and Duck are out buying lunch for the other Loonatics when suddenly an earthquake occurs that sinks parts of Acmetropolis into the ground. The team finds that an evil genius named Dr. Dare plans to place the entire planet underground through a series of earthquakes with the help of the Jade Serpent Crystal. The Loonatics must stop him and return Acmetropolis to its original form.
- A new villain named Massive uses his ability to control gravity to commit several robberies all over Acmetropolis. His goal is to use the robberies to make as much money as he possibly can. Meanwhile, the citizens and the Loonatics are getting ready for the championship game of a futuristic sport known as "basherball" at the Acmetropolis World Dome. When Massive plots to steal the basherball championship trophy, the Loonatics head to the game to stop Massive's crime spree.
- The Loonatics encounter Adolpho, a mutated dolphin who uses psychic abilities to brainwash sea creatures and destroy any human-made object at sea. It's up to the Loonatics to stop Adolpho and his gang of killer dolphins from taking revenge on the "surface-dwellers" at their next target: Acmetropolis.
- After the Loonatics' mission on stopping Toby the Pizza Boy possessed by a Bio-Tech Brain Parasite device, Rev Runner's family comes to visit when they want Rev to take over the family business. Rev begs Tech to help him make his father proud. Meanwhile, Rev's father shows so much attention to him that his younger brother Rip, the oddball of the family, shows extreme jealousy towards his brother for being the family favorite as well as super hero. When Rip finds the confiscated Bio-Tech Brain Parasite, it takes control of him and acts on his dark feelings of rage and jealousy towards Rev, and the Loonatics must stop him.
- The Loonatics must battle Time Skip, a villain who can control time, and stop him from stealing the Trolbot 9000. However, the Loonatics keep failing while the day resets.
- Drake Sypher possesses the power to absorb the abilities of anyone that touches him, and decides he should be the one person getting the fame and glory of being a hero. He first steals the abilities of a star "basherball" player and scores the winning shot, then steals Ace and Rev's abilities since the two were in attendance at the game. After Zadavia assigns Lexi as the team leader and sends the Loonatics to stop a dam from bursting, Sypher battles the team and adds Lexi and Slam's powers to his. Danger assigns himself as the team leader while Tech creates suits that give the powerless Loonatics simulations of their powers, and make them resistant to Sypher. But in the ensuing confrontation, Sypher steals Tech and Danger's powers, resulting in a completely powerless Loonatics team forced to stop Sypher and get their powers back.
- Massive, Mastermind, Sypher and Weathervane are broken out of prison by Optimatus, and join forces to aid their mysterious benefactor in defeating the Loonatics.
- When Rev and Lexi tamper with Tech's X3000 Automated Weapon System mistakening it for a video game, Melvin the Martian comes to Acmetropolis to destroy it after his spacecraft was hit by a missile from Tech's invention. When Melvin threatens to shrink the planet, Lexi admits she tampered with Tech's invention and Melvin orders that Lexi be handed over to him in 24 Hours. Can the Loonatics find a way to thwart Melvin before Acmetropolis becomes the only planetary location to be "hard to find on any map."
- A popular intergalactic circus featuring unique creatures from across the galaxy comes to Acmetropolis to entertain the citizens. Unbeknownst to many of its inhabitants, the circus contains creatures that are combinations of human DNA and animal DNA and its host, Ringmaster, is the one behind the odd creatures being in existence. When a child disappears and an investigation shows that the last place he was found was the circus, the Loonatics follow a strange monkey-cheetah hybrid to the circus to see what they can dig up. However when the team gets to the circus they find that they are on the list to join the Ringmaster's menagerie. The team is transformed by the Ringmaster and begin their quest to get back to normal and shut the Ringmaster down. After returning to their original forms, they learn that Otto, the Ringmaster's assistant is really the one behind everything. And to make matters worse, Otto transforms the Ringmaster into a monstrous hybrid.
- Mallory Mastermind, formerly Mallory Casey, is a former university classmate of Tech E. Coyote. She breaks out of prison to get revenge on Tech for ruining her attempt to steal knowledge for the university professors. To make matters worse, Mastermind breaks in to their HQ and turns all their technology against them. Tech and the Loonatics must stop Mastermind from inside their own base.
- During a fight against Massive who has escaped from prison, the Loonatics battle the high-tech hunter named Electro J. Fudd who is hunting Ace. However, Massive is actually a robot decoy and soon Electro becomes a target along with Duck to be added to someone's collection.
- When one of Tech's weapons goes haywire causing Duck to take out the Sagittarius Stomper, he vows to revenge on Duck. The citizens consider Duck as the one who did it which make the others jealous. Meanwhile, Dr. Dare is released from his statue prison after being hit by Tech's invention and steals the Shield of Perseus. When Tech is finally given credit, he, along with Duck, are made targets by the Stomper, who is somehow able to drop heavy objects on them while still in jail.
- Pierre Le Pew convinces Slam and Duck that Slam can become a champion fighter in his private tournament. However, he fails to tell them that the last match is to the death. It's up to the rest of the Loonatics to save Slam before it's too late.
- Now that Optimatus is free, he alongside General Deuce and Rupes Oberon plan to use Planet Blanc's wormhole generator to take over the universe. Planet Blanc is said to be at the center of the universe, and that every point in the universe can be instantly travled to with ease from it. The Royal Tweetums contacts the Loonatics for help. It turns out that Tweetums evaded capture. The Loonatics must find him before Optimatus does, but not without help from an old enemy.
- A series of attacks on Acmetropolis is being perpetrated by felons who work in shadows. Zadavia dispatches the Loonatics and find the culprit is Black Velvet, a woman who was forced to live in darkness after her eyesight was nearly obliterated by the shockwave unleashed by the impact of the meteor. She steals the planet's Doppler weather radar system dish to create a device to shroud the entire planet in a permanent darkness. Along with this, Tech is kidnapped and brainwashed by Black Velvet to help her complete her task. The remaining Loonatics must rescue their teammate and stop Black Velvet. Meanwhile Duck is tired of technology and makes with a bet Tech that he can't go one week without technology
- The Loonatics have to transport Tweetums, the heir to the throne, to his home planet of Blanc to end a war. Little do they know is that they are threatened by a force named Sylth Vester and an unknown figure. Both will stop at nothing to see that the Loonatics don't complete their mission.
- After Paula Hayes, an up and coming weather girl and assistant to current and incredibly mean weather girl, Misty Breeze, is struck by lightning, She becomes Weathervane, a super villain with control over all forms of weather. She launches wave after wave of cataclysmic storms and the Loonatics must stop her before Acmetropolis is destroyed.
- After receiving a message containing clues on Tweetums' whereabouts, the Loonatics and Sylth Vester seek out where Tweetums is. Meanwhile, General Deuce and Optimatus begin their plans to conquer the universe. However, Deuce betrays Optimatus, who joins up with Zadavia and the Loonatics. During the final battle between Deuce and Ace, Ace banishes him to another universe. The episode ends with the Loonatics realizing they have graduated from merely protecting Acmetropolis, and are now protectors of the entire universe. The team decides to relocate their headquarters to Planet Blanc, which will allow them to instantly reach any troubled spot anywhere in space. Series Finale.
- The citizens of Acmetropolis are celebrating the Loonatics on the one-year anniversary of the meteor strike, when the sky is suddenly filled with pieces of rock falling from the stars. An investigation by Tech reveals that another meteor is headed straight for Acmetropolis, only this one is 500 times larger than the one that gave the Loonatics their powers one year prior. As the team prepares for the intercept mission, we see learn about each Loonatics' life and what they were doing before the meteor struck: Ace was martial arts stunt double, Lexi was a student at Acme University trying out for the cheerleading squad, Duck was a pool boy, Slam was a professional wrestler, Tech was a student at the Acme Tech Institute, and Rev was a delivery boy/inventor. When they fail to destroy the meteor, they land on it to plants charges and destroy it from the inside. Though successful, an unknown figure declares he will destroy Acmetropolis despite two failures of using meteors.
- An old friend of Danger Duck, Officer Pinkster Pig, helps the Loonatics in their fight against gangsters Stoney the Stone and Bugsy the Bug. But since he helps, things have been going bad for the Loonatics.
- The planet is in the grip of Fuz-Z mania when a cute little creature becomes one of the most popular pets in Acmetropolis thanks to Professor Zane, who says that he found them shortly after the meteor strike. The pets become so popular that even Lexi gets one for herself. But when an attack occurs involving a mysterious creature, the team suddenly learns the truth that the Fuz-Zs are the attackers and are spurred on by eating chocolate, causing them to grow and attack. The Loonatics enact a two-step plan to get the creatures out of Acmetropolis while stopping Professor Zane.
- Zadavia explains the history of herself and Optimatus to the Loonatics. Optimatus betrays Massive, Mastermind, Sypher and Weathervane, sending them back to Acmetropolis as he activates a Wormhole to suck the city-planet up whole. Now knowing the secret of his past and his relation to Zadavia, the Loonatics head for Optimatus' base of operations to battle him and his "Optiforce" once and for all!
- Landing on the island of Apocalypso, the Loonatics find a colony of beautiful, powerful women called the Apocazons led by Queen Athena. Queen Athena was impressed by Lexi's behavior towards Duck, and invites her to join them in a very special event. However, not all is as it really seems with the Apocazons.
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