The threat that Spectrum have been awaiting for had to come, and Cloudbase being the principal headquarters of the organisation makes it an obvious target which would make seizing control over Earth a lot more easier for the Mysterons in order for them to complete their raging war of nerves, so the "aircraft carrier in the sky" is targeted for destruction.
With Symphony Angel stranded in the desert due to an unknown explosion on her Angel Interceptor, forcing her to eject, Captain Blue especially becomes agitated, for obvious romantic reasons, at the fact that she could die.
With instructions for any aircraft entering a 100-mile radius of the airbase to be destroyed, and itself sealed from all external contact, the Mysterons themselves decide to visit Earth to obliterate Cloudbase personally, making this threat the most vengeful of all their past avengements.