You take missions in the bunker every time with the officer. These missions have a date expiration, so when you return in the bunker before the end you must then re-take the same mission, or chose other mission areas if there are more of them.
Be in open sea just BEFORE the mission end, and you will get notified of the war progress and you can then start a new chapter.
Also during your patrol, you may get special instructions. Read your Captain's Log and incomming messages.
To know how TWoS works, you must read all here:
http://www.subsim.com/radioroom/showthread.php?t=210703