When an alien named Doodo mistakes Chris for an intergalactic Emperor, Chris goes along with it, thinking it will be fun. But things quickly get out of hand when the MBC discovers that there is an evil alien named Krungnar who is out to mandelbark the emperor's flaggins.

When Danny and Sam mess up a few assignments, the IGA commander sends down two droids to assist the MBC. But, while Chris and Cathy get along with the new recruits, Danny and Sam suspect that they're up to no good. Meanwhile, Mr. Smith recruits the MBC to help him plan Cathy's "Sweet 250" birthday party.

The MBC investigates a strange caveman-like alien that has come to earth and is reaking havoc around the school. Krog's destruction seems to be random, until they discover what he's really after - the hand of Principal Rollins! Meanwhile, when the MBC decides that Sam needs to "lighten up" a bit, Cathy takes it upon herself to try some strange Rhapsodian techniques.

When Singletown experiences some strange weather patterns, the MBC discovers that the entire town is covered with an alien Jellynerp. The creature was placed there by the local weatherman - actually an alien - who is tired of reporting the weather and wants it to be the same every day. A sound plan, except for one minor detail: now the Jellynerp is hungry and it's starting to eat the town!

The MBC unearths a time capsule left behind by the original MBC, warning of an attack that is due to take place in the future. The MBC receives a series of encrypted clues, which they must follow in order to avert certain disaster - in the form of all the aliens being released from the containment grid! Meanwhile, Mr. Smith's sister Frida shows up for an unexpected visit.

An evil Lizard creature (hell bent on eating the precious Mobotto Flower) performs an alien mind meld on Danny and the two end up switching brains. While Danny tries desperately to warn the MBC, he falls into the clutches of Roy and Ralph who try and make him into a circus lizard.

When Singletown goes into an unexpected deep freeze, the MBC suspects alien activity. It turns out that Pizmo, a reformed eater alien, has turned the town into his own personal workout facility. He's created a cooling machine so that he won't sweat during his insane workouts. But now the cooling machine is out of control and threatens to throw Singletown into another ice age.

When Jeremy accidentally comes in contact with an alien substance, he undergoes a strange transformation - turning into a hideous monster whenever he sees anything Rhapsodian. The MBC must figure out how to reverse the effects before Jeremy destroys everything. Meanwhile, Sam gets blamed for injuring Mark and Rollins forces her to assist Mark with his hideous science project.

When the MBC breaks the record for "monsters busted in one month" they receive a reward from the IGA commander - flying lessons on the ultra-cool V-9 spacecraft. But, as it turns out, the flying lessons are all a ruse. It's a plot by their old friend Herptilius to kidnap the MBC and ship them off to an intergalactic barbecue... where they will be the main course!

Glutin the Sticky alien returns to Singletown Middle School and he's out to bag himself a Rhapsodian. The MBC immediately assumes he's after Cathy, but they're mistaken. You see, during a mishap in Fuster's class Cathy's powers have inadvertently been transferred to Wendy! The MBC has to try and reverse the effects before Wendy gets out of the school... or gets captured by Glutin!

The MBC investigates when people start mysteriously disappearing all over town. It turns out to be the work of "Beady" - the evil twin brother of the speed morpher, Speedy. He's determined to set up a museum-like exhibit of "The Galaxy's Strangest Creatures" and tour around the universe.

Mr. Smith surprises the MBC with a special performance by a great magician - Rhubarb the Remarkable! However, the gang is shocked to learn that Rhubarb is actually a "reformed" bad guy that they defeated in episode 10 - Wedge, the talent agent. They're suspicious of Wedge right from the start... and with good reason.

Mr. Smith puts the MBC in charge of protecting a small black orb. What they don't know is that the orb actually contains an entire galaxy! And things get really tricky when a vicious spider alien confuses the orb with her missing egg! Meanwhile, Mark challenges Danny to a bowling competition on his own private bowling lane.

Mark finds a "training tape" of the MBC kids and tells everyone in school about the alien-fighting club. With their secret discovered, the MBC kids are idolized by some classmates and jealously mocked by others. Several vengeful aliens also learn the kids' identities and set out to destroy them.

While Cathy and Chris battle the ever-increasing Annihilator forces in the present, Danny and Sam are in the past trying to alter the course of the future and prevent Mark from ever getting his hands on the tape. However, their efforts keep failing and, back in the present, the Annihilator mother ship has arrived with its Death-Star-style beam to flatten the town.

An exciting event takes place in Singletown: a solar eclipse! Soon, this exciting even turns out to be more than just exciting: completely weird! The eclipse doesn't end and Singletown become the target of an alien who wants to turn it into a giant night club! At the same moment, Cathy gets assigned a new mission from the commander that she has to succeed if she wants to keep her club membership!

Random objects begin to disappear around Singletown, and some objects end up in the weirdest locations! The MBC investigates and soon discover it's the work of an very tidy alien who's only goal seems to clean up Singletown. All of Singletown is threatened to be turned into a spotless town, humans included!

The MBC embarks on a camping trip to search for a rare alien plant that only blooms once every 200 years and will provide fuel for their MBV. The MBC struggles to survive Mr. Smith's bizarre idea of a camping trip. While in the woods, they also discover an evil alien who's searching for the same flower.

The demands of the MBC force Danny to duck out of several "tough guy" challenges by a new kid at school (who turns out to be an alien intent on disrupting the MBC's teamwork). Meanwhile, Cathy runs for student council president.

The MBC goes up against Herpitilius, a giant frog from outer space. Herpitilius was originally an earth frog who nearly got cooked up in a French restaurant, but managed to escape. He was abducted by aliens and turned into a super frog, and now he's returned to round up his earth brethren and exact his revenge.

The MBC encounters a weird-looking alien, Mimi, who seems to get everything ready for a wedding in Singletown.

A group of bubblegum-like aliens come to earth to seek refuge from their planet (Bagumblia) which is suffering from global cooling. Their leader is angered when Danny inadvertently chews him and declares war on humanity, taking Mark as their hostage. The Baglumbians threaten to unleash their hideous mastication monster on Mark, and the MBC must leap into action to protect him.

While looking through some old MBC artifacts Chris inadvertently brings to life a statue of Addison Single that stands in front of the school. It turns out that Addison (thought to be the town founder) was actually an evil alien that was "statue-ized" by a colonial version of the MBC.

The MBC are charged with protecting an alien ruler who is a tiny flower, but Jeremy naively takes the plant as a gift for his secret crush (Cathy). Meanwhile, Sam gets addicted to Chris' video game.

Various things start disappearing around town, but nobody sees where they're going. By slowing down surveillance cameras, the MBC discovers that a "speed morpher" is stealing all of Singletown's technology. If he isn't stopped, the town will collapse into chaos - and the MBC kids will all lose their new part-time jobs.