Probably fiction. The NSA might use its black budget to fund tough guys (paying the payroll and overhead), but they'd probably be trained and managed by the CIA

Probably fiction. The NSA might use its black budget to fund tough guys (paying the payroll and overhead), but they'd probably be trained and managed by the CIA and / or military, as part of some joint operation. It's very common for public officials to get too much money, and not be able to spend it. So they find another agency which wants the money, and organise some kind of joint operation. It keeps their spending nice and robust (so the bean counters don't realise they don't need all that money), and the other side gets the resources they need. It's win-win (for everyone but the taxpayers).