Hmm, this sounds a little like my first experience, getting plastered by pirates time after time and nowhere to run but the nearby shop that was out of everything needed, even core's. :D
I also left the game alone for a few weeks, until I found one could reset the server to a fresh state. I actually uninstalled and reinstalled the whole game to accomplish that the first time before I knew it could be done in the Launcher as well. I then noticed in the launcher one can set the pirate AI to easy, so I did that. This setting is something to keep an eye on though, because every startup this field in the Launcher defaults to hard, so be wise and reset that to easy as long as you're not comfortable with more difficulty.
Greets,
Jan