Always save your game before entering port. It lets you start from that point, and if you don't want to get re-assigned to Pearl, just reload the game, wait for the icon to end the patrol, and when offered a new command, you can decline it. Usually, the next time you get offered a new boat, the Gato will be it, but you will stay in Brisbane. But just to be on the safe side, save before you enter port.
Once I get to Brisbane, I like to stay there. Wish we had Guam as base. So that by '45 we could move up closer like they did to the action. No need to stay in backwater port when the action is 3,000 to 4,000 miles away. Burn up half your fuel just getting there, let alone going home.
One thing that is kinda odd, I finally took a Gato boat, and as usual, I had to load it up with all the gear needed, but the SJ radar wasn't showing as available, even though i had it on my last boat, a Sargo.
So I saved the game there in the captain's office, exited the game, and just for the heck of it, I went to equipment page in the office, and low and behold, there was the SJ radar.
I think some ensign in command was up to some tom-foolery or something.