The series takes place in Cyberspace, a virtual world, and chronicles the adventures of three children, Jackie, Inez, and Matt, as they use math and problem solving skills to save Cyberspace and its leader, Motherboard, from The Hacker, the villain.
Professor Archimedes has the encryptor chip, but has to activate the emergency defense system when Hacker arrives to steal it. He and his building shrink to 2D, and the kids and Digit have to put him back to 3D.
Motherboard is suddenly sickened by the green liquid because of Buzz and Delete. So it's up to Digit and the kids to heal her using blue liquid.
Hacker challenges the kids and Digit to a game show entitled "Find Those Gleamers!", Gleamers being lightning bugs that power ships such as the Grim Wreaker. The kids have to make their ship, the Grim Wreaker 2, take off before time expires.
Hacker steals the cyber slug Icky to destroy Aquari-yum, and the kids make a code to fool him.
Hacker steals all the water from Sensible Flats to buy up their land, and the kids must determine when this started and how to fix it.
After Hacker kidnaps the kids, he crash-lands in Shangri-La, where Master Pi challenges both groups to a special contest. The winner is free to come and go at will, while the loser has to stay in Shangri-La until they learn to solve the problems.