Josie Trent arrives at Blake Holsey High shortly after the school's science teacher, Professor Middleton, mysterious disappears apparently as a result of a wormhole (also called a "black hole" or a "vortex"). When she and Corrine are also sucked into the wormhole, and find themselves in Pearadyne Labs on October 4, 1987, the day of a major accident.
Marshall, feeling unappreciated, turns invisible. Although he has fun at first playing practical jokes, he doesn't enjoy the experience anymore when he discovers he is fading away.
A magnetic field develops around Josie after an accident with her and Corrine's science project. She has fun attracting metallic objects to mess with a popular girl until her powers grow out of control and she becomes untouchable.
Corrine repeats what she considers the worst day of her life over and over, in a manner similar to Groundhog Day. The loop only ends when she is able to look at the day optimistically.
After being bitten by a mayfly, Lucas's genetic code is altered so that the aging process is rapidly accelerated - similar to that of a mayfly. Despite enjoying the freedom of being an adult, he quickly learns that there are disadvantages to growing up too fast.
Vaughn accidentally changes the present when he and Josie travel back in time to 1977, preventing his parents from meeting (similar to Back to the Future). When Josie comes back, she's not a student at Blake Holsey, Victor is the science teacher, Professor Z is a fry cook, and Vaughn doesn't exist. Josie must restore the relationship between Victor and Sarah Lynch to change Blake Holsey High back. During that process, Victor steals Josie's the floating Qigong ball.
A clone of Josie is created from saliva on her chewing gum, which further strains Josie's relationship with her mother when Kelly Trent comes by for an unexpected visit. The clone is sent elsewhere through a vortex (not the one in Professor Z's office) by the Janitor, to another place where she belongs and where "friends are waiting for [her]".
Lucas finds a radio receiver picking up signals from the future, which is found out to be from Pearadyne Labs. The radio picks up warning of disintegration of the school by ultrasound (from Victor's demonstration), and later compulsory purchase of the school by the government. To save the school, the Science Club devise a plan to evacuate the school and divert the media.
When Victor asks Vaughn to spy on the Science Club, Vaughn's emotions manifest themselves in a series of localized storms, which can only be resolved when he releases all the pressure inside him by defying his father, and telling the truth about Josie's stolen journal.
Professor Z narrowly escapes being sucked into the black hole, but loses a huge part of his memory in the process. The Science Club must restore his memory before his semi-annual Teacher Review, which if he fails can lead up to his termination. At the teacher review, Josie, Lucas, Vaughn, and Marshall get busted helping Z as students are not allowed to attend teacher reviews, leaving Corrine to save the day.
Odd magnetic field effects cause Josie and Vaughn to lose their way in the forest while searching for the Pearadyne Labs building. As Principal Durst and the rest of the Science Club seek the two missing students, Josie's need to find the lab causes Vaughn to twist his leg.
Josie surprises everyone by completing her robot building project. However, when Josie uses circuit boards from Pearadyne, the robot takes on Josie's personality and behaves chaotically during an inspection by Pearadyne labs.
Josie laments her short height, but is then shrunk to a far smaller size. She uses an answer machine message to prevent Victor from selling Pearadyne Labs, and learns of a strange operation taking place on the school, covered up by "Blake Holsey High's first compulsory pizza and movie night." The students create a diversion to get out of attending the mandatory school function and observe the inspection.
Josie gets sucked into a vortex, sending her three hours into the past. If she doesn't enter the vortex when it is time, she will be stuck in an alternate dimension. Meanwhile, Josie's mother thinks about cooperating with Victor.
When Madison runs for President of the Student Council, Josie runs against her for the sole purpose of defeating her. Josie promises to change the system of grading, while Madison uses pheromones to capture everyone under her control.
Marshall is going about the school with a cold, and his sickness spread via wireless computer networking to the entire school with chills, fever, and sneezing. People who have purchased a special computer system that allows them to surf the web are demanding refunds when thick mucous is disrupting the system.
A class DNA project goes awry when Lucas' DNA is altered and his personality changes from a bookworm to being absolutely fearless, but lacking self control. His friends must save him from Stu Kubiak, who calls a fight with him.
When Lucas decides to measure Vaughn's brain activity with an EEG machine, their two mental states are switched, with Lucas' brain in Vaughn's body, and vice versa.
Marshall's older brother Grant comes to town when applying for a job at Pearadyne, but an accident with molecular models sends Marshall through the periodic table, into helium, oxygen, neon, chlorine, and on the path to uranium. Meanwhile Grant becomes sodium as he arrives at school. The two eventually meet, and are turned back to normal by forgiving each other, producing the stable molecule sodium chloride (table salt).
When Josie takes Corinne's music CDs for a surprise birthday gift, a rumor starts that Josie is a kleptomaniac. However, the rumors are also correlated to Porifera sponges reproducing at an abnormal rate.
Marshall finds old SIM cards in the basement of Pearadynes Labs, and produces a homemade mobile phone. The chips contain powerful encryption technology which Marshall explains to Tyler. Subsequently, Tyler threatens Marshall into helping him cheat saying he will help him with his sales. Using the encryption technology, Tyler sends an emoticon (:-X) to Marshall, causing all communication to come out as meaningless gibberish. When Durst accuses Marshall of cheating, the others must get him to talk normally so he may speak in his defense.
In preparation for Burton J. Zucherman Science Olympiad, Corrine chastises the Science Club for incorrect equations. When she alters the equations, the other Science Club members manifest into those equations - Lucas' luminosity equation causes him to glow like a firefly's backside, Josie is defying gravity, Vaughn has unlimited momentum, and Marshall vaporizes.
When Corrine auditions for Magnet 360 (Marshall's band) as a singer, she looks at an antique mirror, through which she travels. Everyone there is opposite (for example, Vaughn, the athlete, is a bookworm) and everything appears as a mirror image (i.e. whenever she would normally, say, go left, now she must go right). To return, Corrine must learn to use the creative half of her brain without losing her ability to use her logical side.
Students are becoming addicted to energy bars, especially Lucas and Vaughn, who aren't willing to give them up. The others must attempt to save them when it is discovered they contain zero calories or energy, thus weakening the addicts.
When Josie's hearing becomes super-sensitive, she overhears Victor underground talking about running tests and investigates with Vaughn.
Josie's watch acquires the ability to stop time, which she uses to take back the Chi ball that Victor stole in 1977. However, when her watch breaks, Lucas ends up saving her when he realizes that the watch does not stop time, merely slow it down greatly. The damaged parts are spun on a high-speed centrifuge, bringing Josie back to normal. However, her clone, who has obtained the stopwatch, stops time again and gives the Chi ball back to Victor.