Well... to keep with the whole central computer being a server for a massive army controlled intrinsically by a select few experimental soldiers, why not make it an algorithm? A code that when applied to a database is able to direct and render usable a nearly infinite amount of information. This could bind into the army and "souls" in that a code this complex was necessary to interface with the Master / Slave protocols of the units. They had the ability to take Slaves (but would, by necessity, be the last step as kidnapping thousands would be suspicious) and the ability to make Masters (which was already done) but couldn't link them without the Code.
How's that sound?
Also... the H-Bomb? I hope you don't mind the change.
"Wait a minute here," Marcus said as he quickly recovered. "What's going on here? We're going to just sneak into the Cheyenne Aerodefense base with a prisoner and do... what exactly? At best this would be a suicide mission, at worst... And what in the world would we need Darcy for? You know, the Hydrogen bomb?" Marcus was proud that he'd been able to follow most of this, but it was mainly a series of flukes. Being a data miner, he knew where and how to look to figure out some juicy secrets, but he only had some cursory knowledge of what was going on. "You know what, while we're on the subject, how do you two know each other?!"
Otebon immediately dropped his eyes in embarrassment. "I'm sorry Marcus, I should have told you earlier. A long time ago, Mark and I were part of a group that I'm not allowed to tell you much about. I was the team's medic, he was our..." Otebon glanced at Mark and he jumped to fill the void. "Hacker". Otebon sighed. "I'll live with that. He was our hacker. It was our job to stop bad things from happening, and we were pretty good about it until we were betrayed and we both had to go underground. As for Darcy... Darcy was something that Mark had the original idea for actually. It is a Hydrogen bomb, but modified and changed in such a way that it is very controlled. The power of a sun with a kill radius of about 100 yards. It's the perfect sabotage tool as it completely atomizes it's target. We need to get it so that we can atomize the server unit that will link these Slaves to Masters like Zat over there."