My father, a marine diesel mechanic (who is much more qualified to be the engineer on that ship than the actual "engineer" was) suspects it was the first real weather they'd been in in a long time. The waves stirred their tanks and clogged their fuel
filters, which killed the generator and engines. After that it isn't long until the pump
uses up whatever battery power they have left. Pump
may have even been clogged by stuff in the bilge that got stirred up by the waves.
Probably could've saved the ship with a couple fuel