Season 2

Ace meets a mysterious young man, Deuce, who saves his life when Ophiuchus Sam attempts to rob an interdimentional train. But Deuce is not who he appears, and Ace learns the true origins of his sword.

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.

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.

The Loonatics have to transport Tweetums, the heir to the throne, to his home planet 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 they don't complete their mission.

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. When Rev's brother Rip finds the confiscated Bio-Tech Brain Parasite, The Loonatics must stop him.

Stomper is on the loose, and it is up to Danger Duck to fight against this new villain.

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 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."

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.

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 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 theme song for Zadavia on Freleng, but was shot down since there already was a theme. He uses the guitar to steal all of Zadavia's powers.

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.

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.