Those cutscenes are just a little flavour of what was going on in the pacific war. So are the "fox" reports you get constantly in your radio, which will be comenting things as irrelevant (for a sub skipper in the pacific) as the soviet victory in Stalingrad.
None of this is supposed to give you insights or directions on what you should be doing in the sea.
However the game does replicate the most famous engagements of the war, so if you happen to be near one of them in the correct date, you'll see it - and maybe take a part in it.
But what you're really required to do is to fulfill your mission assignment - which can be varied as droping agents and cargo in specific areas, attacking specific task forces, patrolling specific areas for merchant shipping - as well as sinking all targets of opportunity that may come in the way.
As Razark said below, you do not get penalized that much not fulfilling mission goals - as long as you get back alive with little damage and a beautiful hit record.
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