If your boat sunk a couple of thousand meters then you should be looking at a screenie of a statue commemorating your sacrifice.
If your engines just stopped working,for no apparent reason, my first thought is that you went to Battle stations and did not remember to secure from Battle Stations. This would cause your crew to become fatigued beyond their ability to continue manning the boat.
There have been threads though about mysterious engine stoppages..with no cure that I recall other than relaoding a past save. This could also be the problem.