Defeated, but not destroyed.
Master Control was down to a hundredth of his power, his armies scattered and routed. His champion, Sark, destroyed. His lackey Dillinger led out in handcuffs and his face broadcast all over the six o'clock news. The system had gone back to its annoying Blue, Programs celebrating and believing him gone. Encom was now firmly back under the control of Gibbs.
Flynn distracted him when he was already expending too many resources to fight Tron. He expended those resources because Alan Bradley had been able to access the system. The chaos started at Lora Baines's terminal. The only option he had was retreat.
It took the combined efforts Program and User to defeat him. It also took multiple Users.
Separated, Flynn, Baines, and Bradley could be thwarted. Together, they were a threat.
He would have to separate them, pick them off slowly and in separate attacks. Make it look like a series of accidents and tragedies. Doctor Baines and Yori could perish quickly. Flynn was foolhardy, that would require setting a trap. Tron could be overpowered, maybe compromised through malware. Bradley was the hard one; he could think like a program if he had to. Master Control underestimated him most of all.
Alan Bradley would have to die last. He would have to watch the others fall.
He had little power, and most of his access was cut. Yet what he did have was a cache of secret bank accounts scattered all over the world, a lot of time, a lot of patience, and the fact his enemies believed him to be destroyed.
When human Users rebuilt their networks, he would be there. He would change his plans, be quiet about his infiltration, poison the networks without their knowledge. From there, it would be a matter of finding and seizing opportunities.
Humans would only become more dependent on the digital world, on its networks. As those networks and systems grew, so would he. Overt conquest failed, but maybe a slower, longer, and silent game would prevail. As long as his enemies thought him de-rezzed, he could work with impunity.
He was only defeated, after all. His enemies would be destroyed. They just didn't know it yet.
Perhaps taking over Encom was also an incorrect tactic. Perhaps he should make his own company to compete with Encom. He had the money. He could easily get a few humans to act as his minions, use its resources on the User side of the screen to help bolster his position. It needed a good name. Something banal, bland, beneath suspicion…
Future Control. That's what he was going to do, control the future both in here and out there. It had a nice ring to it; Future Control Industries.
Master Control set to work. He had a company to build.