In a computer world named Cyberspace, in a high-tech center named Motherboard Control Center, technichian Dr.Marbles, along with his assistant Digit, are giving the computer ruler of Cyberspace known as Motherboard, a routine upgrade on her circuits.
Meanwhile, watching Dr.Marbles upgrade, is someone who worked for Motherboard in the past, Hacker. Hacker, in the present, is the most evil and mean being in Cyberspace. Watching Motherboard get upgraded from his ship, the Grim Wreaker, Hacker downloads a virus to Motherboard. Dr. Marbles and Digit notice Motherboard got infected with a virus and Dr. Marbles gets captured looking for a cure for Motherboards virus.
Meanwhile, on Earth, three kids named Matt, Jackie and Inez have met up at a library. While staring at a screen, Motherboard appears on it and the kids find out she knows their names. She disappears and a portal appears and sucks all three in.
Matt, Jackie and Inez end up at Control Central, to get a item called a squawk pad. Digit then greets them and Motherboard says Dr. Marbles got kidnapped at an island called Topsy Turvy island.
Digit and the kids arrive at Topsy Turvy island, and find out that every once in a while there is an earthquake and when the sun sets, the island will reformat.
Digit and the kids use ordering pairs to find out how many paces to Dr. Marbles. They do succeed and find Dr. Marbles, but they must find a way out of the island before it reformats. They find the Grim Wreaker parked, but when they start it up, they find out safeguard is on. Dr. Marbles uses his one-seater cybercoupe, which he used to find a cure for Motherboard, to exit. Motherboard was able to program three exit portals on the island for the kids and Digit. They decide to go to one of Motherboards portals on a river, using a raft. However, Hacker tries to stop them using the wreaker but the kids manage to raft into the portal. The Hacker, finds out the sun has set and is trapped in a dome of ice.
The kids, however, end up at the library.
They are back at the screen in the library, when Digit and Motherboard say that Hacker is still out there.