If you're getting an option to ABANDON MISSION, it sounds like you're playing a single mission rather than in career mode.
IIRC, when you're in single mission mode you don't have the same options when you select EXIT PATROL. Selecting a single mission to play means you've gone out on one single patrol with a specific objective. When you decide to end the patrol, the mission is over (whether you achieved the objective or not); if you select Abandon Mission, your only options are to confirm the Abandon Mission order by returning to base (which ends that gaming session until you reload a mission or career) or belay that order and continue on the same mission.
It's not an open-ended situation like career mode, where you go out on one patrol after another and "docking" is just a break between two of them.
My apologies, the directions I was giving assumed you were in career mode.
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