I think you have to try to sink a ship close to the mission icon on your map. Every now and again you will get s message from BDU telling you to reposition and continue. This means they have moved the mission icon to a different place in your patrol area.
Just have a look on your map for it. Eventually you will sink a ship near it and then in a bit you will receive another message from BDU stating "Cease all operations and return to base"
Then you head back
