Very good Commander,
You are and will continue to be Naval officers, there is no need for a transponder change, you'll simply be taking orders from the Agency's chain-of-command. You and your squad will continue doing your job as Naval officers, however at times the Agency will direct new orders to you that will overwrite the Naval chain-of-command, most of these operations will be classified even to your superiors.
Now for some ground rules. Your orders at the time -if any- will be given directly by Tac Ops operatives of the Primary Directorate, if they have the authorization they will contact you with certain authorization codes -which you'll be receiving shortly- before anything, in short, you don't answer to the entire Agency, only a select few. You've already been given a hangar aboard Hoover Station, I don't think I have to say that anything you or your men see, hear or even
feel there is strictly classified. Your equipment and ships will be taken care of by the Agency on military-level standards. We don't care about the
martial competence of your men, they need only keep a secret when ordered to.
If any...unforeseen problems occur in the aftermath of an operation, be they political or internal you are to make sure they don't lead back to the Agency in any way. If anything problematic occurs with other Naval forces due to your orders from us, all you need is drop a communique, we'll take care of it.
Now for your standing orders.
Quite a bit of classified information goes through Hoover Station and even more is saved there. Recently however we've been using even more bandwidth as more memory is allocated to operations, which makes the security of Hoover Station an even more important fundamental to Liberty's own security.
As such, the Torpedo squadron is to keep a strict defensive line for Hoover, you are ordered -and- authorized to
destroy any and all Non-Liberty-Armed-Forces vessel that show -any- kind of hostility towards Hoover.
Other than that, continue doing your jobs as Naval officers, if anything else comes up, we'll be in touch.
Your have your orders Commander.