What a great setup! This story is rich in description, in atmosphere and suggested calamity. You bit off a lot, for a short story. This is great material for a larger piece. As it is, so much happens so quickly that you don't have time to develop some serious aspects of the piece. For example, you jump to the conclusion that this is the 'last ship'. Yet, there are others ships sailing to safe waters. When the people on board see a lack of activity they immediately suspect something sinister, and rush to collect food. Why do they imagine, so quickly that there would be a food shortage. This is a leap that would not likely take place so quickly.
This is a great story, almost a scheme for a larger story that could be filled out.
Nice writing, @zerah.