“I know what you're going to find,” Wilford replied, his voice thin and tired. “Axius was one of our―the Confed's, rather―centers for 'black budget research' during the war. The system is barren, no biosphere whatsoever. It's the ideal place to test weapons, especially bio-weapons.”
“How do you know about it?" Blair asked.
“I was briefed on it when I took over the sector command just before the war ended.” He took a deep breath. “It was supposed to be shut down after the Kilrathi War. Apparently it wasn't ...”
The last we hear about it is page 309, when Blair runs after his cover's blown. The fortress' smaller guns were already registering as he oriented his fighter towards the lane through the minefield. A single laser bolt hit his aft phase shield. He cloaked, jinked, and ran like hell for the Intrepid.
It's possible that there was no need to destroy Axius. As Dundrdal mentioned, it was an existing black ops base set up by the Confederation... Tolwyn was just using it for his conspiracy, just like he used the Lexington and the Vesuvius. (We know it wasn't entirely crewed by Tolwyn's GE soldiers--the novel mentions that a guard on the base recognizes Blair from having served with him on the Concordia.)
I guess you have to liken the whole thing to World War II (as was intended)--the only true bad guys are the Nazi leadership... the men in the ranks don't necessarily know that there's anything wrong going on. They're following their orders and as far as they know serving their country... and 99.99% of them probably have no idea what was happening at places like FT957.
(In fact, imagine it this way--what if after Special Operations 1 it was revealed that Tolwyn had engineered the whole situation with the Gettysburg as part of a plot to murder her captain. We wouldn't need to hunt down Blair or the Concordia crew--they had no way of knowing what was going on and once the truth came out would be unlikely to go rogue or anything like that.)