I have no idea where the line between fan fiction ends, and obvious copyright infringement. Thee are a few star trek themed games here, but none as bold as "my" projects that rely heavily on art from well known IP's. Am i completely wrong? If there a logical point, then a line? Can I just go forever? What will happen to a project that goes too far?

I'm not a lawyer either. But I guess you are fine as long as you make negligible money. 

If you make money, it's quite likely they'd want a piece of the cake. If you set out for making money I guess the Star Trek thing could be very helpful for marketing. Have you tried contacting them for a license?