Kilokhan is a very powerful and evil computer program. He desires to conquer the world through Cyberspace. He teams up with Malcom Frink. Turning Frink's drawings into Megavirus monsters. He sends these monsters to infect and take over various computer systems. Time and again his plans are ruined by Server and the rest of Syber Squad. Kilokhan hates humans and refers to them as "Meat Things". He often times gets frustrated with Malcom. Kilokhan takes over Malcom's body for a day. But has problems living as a human. At one point he becomes all powerful and turns against Malcom. Malcom ends up helping Sam defeat Kilokhan. But both lose their memories of the battle. Kilokhan is restored when Malcom loads his computer back up files. Who continues to savage Cyberspace.
Malcolm Frink is the school reject at Sam's school. He grows to hate Sam and his friends. And also has no real friends of his own. Malcom is a gifted artist and a skilled computer user. He allies himself with Kilokhan. Who brings Malcom's drawings to life as Megavirus Monsters. He often grows annoyed at Kilokhan but needs him as much as he needs Malcom. Malcom often uses Kilokhan's viruses for is personal gain.
Having an affection for Jennifer ( Sam's girlfriend) he uses a virus to control her mind. Which makes Jennifer do anything he wants. When Sam destroys the virus, Jennifer returns to normal. Malcom uses a virus to change school records and make it seem like Sam and is friends didn't attend enough class. Which forces them to go to summer school. When the virus is defeated records are returned to normal. Which reveals that Malcom is actually the one that needs to go to Summer School. In another incident, Malcom uses a virus to win a Student Presidential election against Loli. When the virus is defeated, a recount is done. Loli is declared the real winner. Kilokhan at one point takes over Malcom's body and traps his mind in a Virus. When the Virus, is defeated Malcom gets his body back.
Later on, Kilokhan becomes all powerful and turns on Malcom. Malcom befriends Sam and helps him defeat the evil program. But memories are soon erased of the battle. Malcom restores his computer, also restoring Kilokhan. Malcom continues to help him conquer cyberspace.