About the first mission with akula

[Rhodes]

I'm sorry for posting this, what do I have to do to end the mission, my radio messages says that I identifided all the rebel threats, then says to damage one big ship, then since I was detected to fire unless to defend myself. The end mission screen says tha the enemy inside the arbour is whiet to be identided. But to enter the harbour I have to came to the surface because its very shallow.
I ask for advice to the top aces heres, please.