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High school student Sam Collins is the head of a band called Team Samurai). During a recording session, Sam is zapped by a power surge and disappears only to reappear seconds later with a strange device attached to his wrist (which is at the time unremovable). Later after his friends Amp, Sydney, and Tanker leave, one of his video game programs dubbed Servo is subject to a power surge and zaps Sam again. This time, the zap pulls him into the digital world and turns him into his creation. As Servo, he roams the digital world and fights monsters called Mega-Viruses.

Meanwhile, another student from Sam's school named Malcolm Frink is designing monsters on his home computer when Kilokahn (an escaped military Artificial Intelligence presumed dead in the power surge) visits Malcolm via computer screen. Kilokahn strikes a Faustian deal with Malcolm and turns his digital monster into a Mega-Virus Monster who is not only capable of corrupting electronics, but is also capable of affecting the real world.

Sam (now as Servo) must enter the digital world and stop Malcolm's and Kilokahn's Mega Viruses. Sometimes, when Servo was unable to handle a virus by himself, he would call on the help of his friends using his Arsenal Programs. The Arsenal Programs could fight the viruses solo, transform (with the help of other Programs) and attach to Servo as armor. Since Team Samurai consisted of only 3 people at any one time (excluding Sam), only 3 vehicles were available at any one time. When Servo linked up with these Programs as armor, he changed his name to either Phormo or Synchro (when he combined with Drago or Xenon, respectively).