The school dance is here and everybody's excited except Lloyd who doesn't have a date until he meets Cindy who is a two headed alien but doesn't know until he sees her at school. He is then terrified but how will he keep taking Cindy to the dance was a bad idea a secret?
Lloyd feels unappreciated by his family and friends, so on the school trip Lloyd and Eddie fall into the worm hole, which takes them to the dumpster 30 feet away. But everyone else thinks they are somewhere else, far, far away, in the universe so Lloyd and Eddie decide this is their big chance and use it to get whatever they want.
After watching a cool movie about surviving in the wilderness, Lloyd and the others ask their dads (Lloyd asks his grandfather due to his dad not being around) to take them to Zoltan III, but accidentally end up on Fangor Dar, the planet of danger.
When school bully, Rodney Glaxer, picks on Douglas and Kurt and challenges the former to an after-school fight, Lloyd suggests Kurt and Douglas work together as a symbiotic boy called Kurtlas, who rids the school of bullies, but with all the fame going to their heads, has Lloyd really found salvation or replaced one school bully with another?
Since Francine's babysitter is somewhere else and Commander Nebulon is leaving the house for the weekend, Lloyd is forced to take care of Francine for the weekend, but it turns into a disaster since Francine is breaking stuff and will blame Lloyd for the stuff she has broken. Lloyd then takes Rosie (Francine's favorite toy doll) and straps onto a rocket ship in order to force Francine to behave. Francine later overhears Lloyd talking to his friends saying he wished he hadn't had a little sister so, causing her to leave the house for good, so Lloyd searches everywhere for her.
Lloyd is sick and tired of school and he sees that he can make an android replica of himself. So he builds it and everybody seems to like the replica of Lloyd even though they don't know that it's a replica of Lloyd until the real Lloyd comes and confesses.
A nerdy new kid named Larvel joins the class, whom everybody immediately ostracizes. Lloyd is forced to help him out, and soon he finds he's a pretty cool guy; but soon he becomes a more physically-developed teenager and starts to hang out with Brittany and the popular kids, eventually ditching Lloyd and his friends.
When this new girl appears in school she makes the boys fall in love with her but they soon realise it is just a trick and only Lloyd is not affected by it, until he confronts her and soon he's affected. It's now up to Cindy to stop her and save the boys from being hypnotized.
Nora Nebulon starts falling in love with the ship mechanic and Lloyd begins to worry about her acting like this he figures out that the guy happens to be a monster like Lloyd thought he was but still then Nora loves him anyway.
The boys have no money and are broke then Lloyd comes up with an idea by starting to do a pet care business. Then Eddie can't take being bossed about anymore and he starts his own pet business which leaves them fighting against each other and soon the pets are all released.
Lloyd is so sick and tired of Francine always reading his mind so Douglas gives his mind scrambler which can block reading his mind but Francine tries so hard they change minds and Lloyd seems to like it inside Francine's mind but Francine seems to hate it inside Lloyd's mind. Will Lloyd in Francine's body save Francine before she gets scared of the dark at Darkon 5 and starts bawling?
Lloyd and his friends try to hide Boomer who is being hunted by Secret Service agents, only to find out that Boomer is not a fugitive but a prince and his father (The King of his home planet) wants his son to come home and to take the throne.
Lloyd's mom and Francine are going to Zizmo Beach which Lloyd thinks is babyish and even worse they are going to McZorks' afterwards. Lloyd declines to spend a weekend with the McNoggins but they are too boring. Then he spends a weekend with the Blobberts but they are too babyish. He then goes to Eddie's family but they are too boring as well. He starts to miss his family and he'd do anything to see them again even if it means going to Zizmo Beach.
Lloyd and friends discover that many of the girls have been getting invitations for a girl's only party at Brittany's house so Lloyd disguises himself as a girl in order to infiltrate the slumber party.
Station's email pen pal is coming over at Lloyd's house so Station asks Douglas to give him a living body just to impress his pen pal and Douglas accepts. They teach him everything to do to act like a man but soon it causes trouble.
During a squabble caused by their inability to get along with each other, Lloyd and his class accidentally trigger a new school safety feature and jettison their classroom into space with themselves in it.
The gang have to do their own chores and get sick and tired of it so Douglas has an idea of introducing them to his Uncle Jubb which happens to live on a farm-like world. They start to hate it as first but soon they start to like the chores that they have to do in Uncle Jubb's home.
Lloyd uses Douglas' latest invention which is The Love Beam and accidentally makes Brittany fall in love with him. He seems to like it at first but then he misses the old Brittany and tries a way to figure out how he can change her back until he realizes that the love beam didn't change her, it only allowed her to admit that she had always loved Lloyd, which she proves by showing him the message she wrote on the same tree as Lloyd, which says "Lloyd luvs Brittany...and Brittany luvs Lloyd too". Though warmed by this, Lloyd eventually still decides to return her back to her conscience, preferring that she wait to reveal her true feelings for Lloyd when she is truly ready to.
The new kid, Zoit, has an upcoming 13th birthday and will then choose to be either a boy or a girl. The boys (Lloyd and his friends) and girls (Brittany, Megan, and Cindy) fight to convince Zoit on which is the better gender of choice.
Lloyd tries to get out of singing holiday songs for Droimatz (their version of Christmas) to read his comic book by claiming he celebrates Theerlap, even though he knows nothing about it. When he finds out there's not much to it, he makes it bigger than it is, and ends up offending his grandpa, the only one who truly knows about Theerlap, by doing so.
Principal Feely wants everyone to find out about their race for a festival and Kurt and Douglas start to dislike each other due to the fact that both of their species have hated each other for generations.
Lloyd and the gang have a plan to scare Francine and her friends at Halloween, topping it off with Boomer's haunted house. But when Lloyd and the gang themselves go into the haunted house they are sent into the future, where all of Lloyd's friends turn into monsters, and he's left hiding on the station for the next fifty years. After admitting he misses Francine, and that he shouldn't have scared her, it turns out that it was a telepathic prank by Francine, with help from her friends and Boomer.
Mrs. Bolt's birthday is coming up and she decides that she has a birthday party but no one wants to go apart from Lloyd and he finds a video of what Mrs. Bolt used to be like rather than she is today and Mrs. Bolt decides she is not going to teach again. Lloyd then shows the tape to everybody at school and they turn up hoping that when she comes back she will be nice and kind to them.
Kurt tries out for the Crater Worm Crush Ball team (their version of football), where everyone finds out that he can remove his head and still operate his body. His body becomes a lot more popular without the head, and rejects Kurt. Around the same time though, Kurt's body becomes mean and unhibited and eventually gets too rough out on the field (even against his own team), and everyone has had enough, making the Kurt's head and body reconcile.
A new kid named Derek comes to Luna Vista and he becomes instantly popular. Lloyd is determined to find out how he is becoming popular and why he feels like it's necessary to take pictures of everyone.
Lloyd becomes commander after a gas freezes every adult in Intrepidville. Soon, everything gets chaotic when Lloyd enables the kids in town to do whatever they want until the adults unfreeze and the station breaks apart, forcing Lloyd to have to save all the kids in Intrepidville.
Eddie reminds Lloyd about an incident from 1st grade that led to him becoming unpopular during his future school years. When Douglas gives him a traveling time communicating watch which will able to take him to any time he wants, Lloyd then goes back to the day he first went to school in Intrepidville to stop his little self from tripping over Rodney's foot and ruining Brittany's picture and he becomes popular in the present. However, Lloyd also realizes that him becoming popular meant that he never made friends with Eddie, Douglas, and Kurt, whom he feels sorry for upon finding out how poorly they've turned out without befriending him, prompting him to go back and restore the balance of time and his former unpopular life.
The class clown and school mascot, Zoopy, is leaving Luna Vista Middle School and holds an audition for a student good enough to take his place, with both Lloyd and Eddie making the cut. But it proves to be even more of a tough competition when the two friends are forced to compete against each other in terms of getting the most laughs for the final test.
Lloyd and Eddie wonder why there is a large crowd of people at a restaurant in the mall and Eddie's Dad tells them that there was a robbery at the restaurant and Lloyd and Eddie go with Eddie's Dad to investigate the crime. This is also the first time that Lloyd gave a warmful advice to his friend, and also the last episode of the series.