What is the deal with Providence?

Solution 1:

As Jake said in a comment, there doesn't seem to be a definitive answer, but I thought I'd summarise what I found in an answer.

There is a lot of speculation on the wiki as well as on reddit. It all seems to point towards the theory that you're actually the evil guy committing genocide on this poor planet, which the Providence tries to protect. Notice that the Providence's "subtitle" is Bulwark of the Weak. Also, if you read through the monster logs, in several of them it is mentioned that most of the "monsters" all seem very social and happy and not aggressive at all until [whoever wrote the log] comes closer.

Some of the posts mention the item logs as well, and interpret them such that your transport vessel was actually looting the planet, which is why the Providence destroys the ship in the intro.

Most of the endings (see the reddit post) also indicate that you leave the planet as a soulless killer. So while you might have initially really just fought to survive (although even by that point you might have been the evil guy who looted the planet), by the end of it, you're just the murdering innocent inhabitants of the planet.

I think it's a really nice perspective on these kinds of games, because essentially that's what you're doing in many games, but you're always presented as the hero getting rid of evil hordes.