When you first get the sub, take it down through the tunnel until you exit into the cavern. Look along the wall to your left to find a small crack, that at the correct angle, you can see another tunnel. Yse your torpedoes and break apart the wall around the crack. You will now be able to follow a tunnel that leads to a cave (with bones lying on the ground), and a brand new sub with full health and full ammunition sitting in the middle of a small pond.