i imagine the Brainiac story line tie-in something like this:
kitty has dropped the kryptonian energy crystals and when NK is launched in to orbit it triggers a reactivation of the energy crystals (the ones kitty dropped), but since it is in space it sends a beacon of as if earth has exploded and it alerts and emergency system that is called "brainiac" (a Artificial lifeform to collect the knowledge for an inter galaxy database that is used to keep records of extinct planets). but when brainiac arrives to earth to collect the knowledge , he finds that earth is still there and that a kryptonian (superman) resides on earth. with NK as brainac's base of control and control of the crystals he engineers them to form minions for a battle against superman to gain control of earth and it's technologly and history as well as Krypton's lose knowledge and information on its destruction( for it was never collected). now minions that have been created with the kryptonian energy crystals brainiac is now determined to conquer earth for its knowledge (for it is in his programing) and to gain information on krypton's destruction. brainiac is now in a fight in space and on earth as well as an artificial world created by brainiac to fight superman(without powers). and brainiac would be ,as brian said of the alein villian, "wrath of Kahn.
that is my idea
Josh Lentz 7/22/06