The Quantum Virus is a computer virus programmed by QAI with the help of Dr. Eric Sweeney who was kidnapped by the Cybrans from Capella. The virus was designed to overload all Quantum gates making them explode. These explosions also caused a wave of quantum energy to spread thoughout the galaxy, making quantum travel impossible for 4.8 years allowing the Cybrans time to recover.

The virus was successfully deployed via Black Sun in the last mission of the Cybran campaign, but this ending is generally considered non-canonical.