Sidney gets a "B" in her report card and she believes it's the end of the world. Malcom decides to plant Scorn into her wristwatch where he will control Sidney's hand. Sidney ends up causing trouble for the rest of the gang.
Sidney and Tanker make fun of Malcom's voice with Sidney's keyboard recorder. Malcom sends a virus named Scorn into the keyboard for revenge, which causes Sidney and Tanker to switch voices. The worse part, Sidney has to perform at the school talent show that night.
Sam and the gang plan a slumber party in the high school to raise money for the state aquarium. Malcolm and Kilokahn send Plexton, a scorch virus, into the school's heating system cause everyone to suffer from the heat.
Malcom sends his newest virus monster into the gangs new horoscope toy causing everyone who uses it to change into their opposite personality. Sam: a coward, Tanker: nerdy, Sydney: a bully, Amp: smart, and Jennifer: evil.
With Servo taking up all of his time, Sam's grades are starting to decline, and so is his relationship with Jennifer. To help out, Sydney creates a program that traps Kilokahn. With no virus monsters to fight, Sam's schedule is free. But will he miss Servo?
Jennifer believes that Sam is unromantic. To prove that he is, Sam plans a dinner for two, with Syndey, Tanker, and Amp as servers and Mrs. Starkey as the cook. To mess it up, Malcolm sends a virus into Mrs. Starkey's oven timer, causing her to go insane. When the gang finds out, Tanker believes that it's time to let Jennifer know what they really do with their spare time.
Amp is in danger of failing his gym test. The gang decides to help train him up for it. Kilokahn takes control of one of Malcolm's new virus monsters and uses it to cause a blackout all over the world. With no computer, how can Servo fight?
Sydney wins a date with TV star Chad Williams. This doesn't sit well with Tanker, who tries his best to stop the date from happening. Meanwhile, Malcolm and Kilokahn send a smog virus to Japan, polluting the sir.
Amp scores highest on the National Scholastic Placement Test and everyone in the school thinks that he cheated. Jealous Sydney finds out that a virus monster has been sent into the test company's computers and messed up the scores.
Malcolm and Kilokahn send a new virus into the school water fountain, which causes anyone who uses it to become paralyzed. When Sam uses it, the gang has to find a day to get him into the computer to fight the virus.
Mrs. Starkey accidentally plays with Sydney's laptop and gets sucked into the Drago program. Malcolm and Kilokahn set a trap for Servo by luring him into the digital world and cutting off the rest of the squad from helping.
Amp gets Team Samurai a spot on the "Bands on the Road" TV show. But at the last minute, Sam gets cold feet. Kilokahn sends a message of challenge to Servo through the TV and threatens to destroy all TV systems if Servo doesn't accept.
The gang is starting to have disagreements. Malcolm plans to use this to his advantage. He sends a virus monster into the school's new security system which causes the gang to be trapped in after hours.
Sam becomes station manager for the school radio. He holds auditions to see who the new radio crew will be and Malcolm tries out. When he doesn't get the job, he sends Skorn into the radio to make anyone who broadcasts spill the truth.
Lucky falls in love with a new girl at school. To impress her, he decides to do magic at the talent show, planning to make Sam disappear, but really Sam goes into the digital world where a new virus monster could mess up the act.
An inspector is coming to investigate Principal Pratchert's work at the school. Pratchert starts to become more strict with the students. To get revenge, Malcolm sends a virus into Pratchert's bullhorn which causes Pratchert to become a teenager again.
Sam Collins and his friends start a rock band so that he can impress his crush, Jennifer. But Malcom Frink also has a crush on her, so when he finds out the Sam has gotten Jennifer's phone number, he makes a deal with an evil computer program called Kilokahn to send a computer virus into the phone lines.
To heal his relationship with Jennifer, Sam decides to write a song about her for the school dance. When Malcom hears this, he and Kilokahn send a virus into one the U.S. defensive satellites to cause a barrier to block one half of the earth from the other. This leaves Sam and the others no way to get to the school.
Lucky has his eye on a new surf board, but is short on cash. Sydney and Mrs. Starkey give him a chance at the lunch cash register. Malcolm sends a virus into the register so it'll look like it's short on cash and making everyone believe that Lucky stole it.
While Sam is working with Jennifer at school, the rest of the gang goes on a nature hike. Meanwhile, Malcolm and Kilokahn's newest virus monster is sucking up all electricity. With no power, how can the gang enter the digital world? And without Sam, who'll be Servo?