> If your systems are compromised and need to coordinate, what do you even do if you can't trust anything, assuming the attacker is still inside the network?

That's a problem regular companies need to write up a plan for (but most of them probably don't put too much effort into it).

Even with the descend into incompetence the USA has been pulling for the past few years, I still expect the FBI to have a plan for exactly that sort of compromise.