So… he had a server installed in his office inside the Pentagon. Nah. Think about the logistics it would take to get the wiring done and connected to it's separate network. First, workers would need to have been escorted into his area and then open the ceilings and add hundreds of feet of fiber.
Anything like that would need to be preapproved by the building custodian and local IT section. It would require a funding code and a contract. All would be easily traceable back. Finally, every area that is not common in the Pentagon is secure. BTW, not saying he's a good guy but this story has a lot of holes.