Basically what I've worked on since before v0.90 I've added a semi-working mod for my v0.90 KSP that adds "AI" to a spacecraft (external part to attach to a craft), then I move the craft somewhere in the solar system. The "AI" basically flies the crafts itself generating random nodes where to go, however they have unlimited fuel and gravity does not affect them. Also due to my poor mod programming using many of them eats ALOT of performance. Since I updated to v1.0 I haven't worked on that mod nor released it because of it's poor performance.
But that's the closest I got in generating an "alien ship"
However this was not done by legit "mod ways"
