Mars is running out of water, and soon the Martian mice will perish. Their only hope is the Regenerator, a machine capable of converting dirt into any substance required (including water). But the evil Catatonians, led by Supreme Commander Hairball, have launched an attack in hope of capturing the Regenerator for their own purposes. Will the Biker Mice from Mars be able to hold out against the Catatonian assault?

With the only Regenerator destroyed, things are looking bad for Mars. The Biker Mice must take General Stoker (creator of the Regenerator) to Planet Earth where he can find the necessary tetra-hydrocarbons required to build another machine. But there is a surprise in store for the Biker Mice on their return to Chicago in the form of developer Ronaldo Rump, who has joined forces with the Catatonians to obtain a Regenerator (the ultimate land-development tool).

General Stoker's exposure to tetra-hydrocarbons has worsened his condition, turning him into the mad "Stoker Rat". He is loose in New York City, where Rump has captured him ito force Stoker to build another Regenerator for Rump so he can become richer. Will Stoker turn traitor? Can the Biker Mice rescue him from the clutches of Ronaldo Rump and get him back to work in the effort to save Mars?

Due to a freak accident Ronaldo Rump is wandering the streets of Chicago without memory (or hairpiece), holding onto the Regenerator. Of course this news makes its way to both the Catatonians and the Biker Mice, who are both chasing Ronaldo.

The Biker Mice turn their motorcycles into radical Swamp Cycles when they discover a mouse damsel-in-distress stuck in the mud. Is this attractive mouse really what she appears to be—or could she be the Catatonian shape-shifter, Catalina Catacall, on a secret mission to trick the Biker Mice into revealing Stoker's secret lab where he is building a new Regenerator for Mars?

The Biker Mice are lured into a secret underground world carefully hidden beneath a Rump Mini-mart where they encounter not only one of the nastiest baddies of all time in the form of the Pit Boss, but an unexpected group of enemies they have not seen for a long time....Lawrence Limburger and Dr. Karbunkle!

Things heat up for the Biker Mice when the infamous Sir Richard Brand-Something arrives with hopes of winning a Regenerator for his own purposes. Joining forces with Supreme Commander Hairball, Sir Richard puts his plans (and his evil robots Bangers and Mash) into action—giving the Biker Mice a ride for their money. In the meantime, General Stoker is finding that the Earth's tetra-hydrocarbons are producing some unexpected (and unwanted) side effects.

Throttle is promoted, and must return to Mars with Carbine; his replacement, Rimfire (Modo's nephew), does not fill his shoes very well, forcing Carbine to rescind Throttle's promotion.

The Biker Mice are arrested and tried before... Judge Ronaldo Rump, which leads to their bikes being impounded.

Throttle is a victim of mistaken identity; an injury leaves him thinking he is a character out of a famous Christmas movie, which leads him to be captured by Doctor Catorkian.

The Biker Mice get their hands on Rump's Regenerator in time to be accidentally transported to Saturn, thanks to Hairball's clumsy control of a transporter machine. With no way off the ringed planet, the mice turn to a race of local hip cats. However, they discover that these wave-riding kitties are descendants of the Catatonians (sworn enemies of the Mice). Will the slick, surfing cats of Saturn turn out to be friend or foe?

The Biker Mice are challenged to a motocross race, where they encounter some serious foul play. As usual Charley uses her mechanical skills to keep the bikes on track, but strange things keep happening. Could it be that Charley is the mechanic behind the mayhem?

Rump hires the felonious Flare to create a landslide inside Stoker's cave-bound laboratory, leaving General Stoker trapped inside and his research vulnerable to discovery. It is up to the Biker Mice to don spelunking gear and rev up their cave-cycles to save the General and his work before Rump and the Catatonians can get their paws on him.

The Biker Mice are reduced to the Minivan Mice from Mars when their motorcycles are stolen by Ronaldo Rump and his evil minions. Just one problem—while they may be the universe's best bikers, nobody ever taught them how to drive a car!

The high commander of the Catatonians has had enough of Hairball and Cataclysm's failure to acquire a Regenerator on Planet Earth, and sends them to the bench. In their place three wily, female Catatonian shape-shifters led by Catalina Catacall are sent to give the Biker Mice a race for the prize!

The Mice discover a race of small rabbits living on the moon, and realize they have new allies who despise the Catatonians as much as they do.

When Stoker discovers Rump has planted a super-virus into his secret computer data banks which contain the secrets of the Regenerator he transports himself into the World Wide Web, intent on killing the virus. But time is running out for Stoker; it is up to the Biker Mice to take out the cyber-threat before they are deleted permanently!

Ronaldo Rump launches his Regenerator into orbit over the Arctic Nature Preserve, planning to turn acres of natural wilderness into Rump Amusement Park! It is up to the Biker Mice to foil Rump's evil plot and preserve this important animal habitat, while taking on the world's top motocross racer on a track designed to keep the best bikers in the world struggling to stay aboard!

Things turn a little wacky for the Biker Mice when Vinnie is accidentally turned into a baby mouse by Dr. Catorkian. If you thought keeping Vinnie under control was a problem before, watch as the Biker Mice attempt to battle the Catatonians and Ronald Rump while struggling to keep Vinnie in clean diapers!

Stoker finishes his new Regenerator and the Biker Mice are ready to take it back to Mars. Unfortunately, Stoker himself has other plans for it even when an unlikely enemy of the Biker Mice poses as a government agent to collect the aliens hiding out on Earth.

The Biker Mice are trapped in Detroit. Their old archenemies Limburger and Napoleon Brie are planning to conquer Chicago with the Regenerator and the aliens in their custody. In addition, our heroes have other things to worry about: Has Stoker switched sides? Meanwhile Charley and Carbine are searching for the Biker Mice, but they meet an unknown mouse from Stoker's past....his daughter Spitfire.

Ronaldo Rump starts a TV show where ordinary citizens can hunt people and bring them in for a reward. This leads to a million-dollar bounty on the Biker Mice's heads, and they have all Chicago after their tails.

The Biker Mice discover they are not the only ones searching for tetra-hydrocarbons when they encounter an educated, soft-spoken Abominable Snowman-type creature named "A-Bomb". But will there be enough to save A-Bomb's family and give the Mice what they need to finish the Regenerator?

The Catatonian shape-shifter, Catalina Catacall, infiltrates Freedom Fighter Headquarters on Mars and captures Carbine. Catalina's objective? To download Biker Mice computer files and get her claws on Carbine's new secret weapon: the Surgerator, a device boosting the Regenerator's power ten thousandfold. However, Carbine is not so easily fooled or defeated and it becomes a showdown between these two enemies with the future of Mars at stake!

Vinnie's crazy pirate Aunt Mago comes to Earth intending to steal its water to sell on Mars.

Hairball hypnotizes Throttle to reveal all the secrets about Stoker and the Regenerator. Fortunately Throttle isn't as easily hypnotizable as Hairball thought he would be.

The Mice finally find Harley, only to realize she hates them because she wrongly assumed they gave up on her. The entire episode is done in the style of a rock opera.