Congratulations you have found a "public enemy" a exiled stargod. They are invisible and this particular stargod has a force blade. If you don't have aye-phones so you can pinpoint his movements run away. Also only aoe weapons like grenade will have any effect. The mechanic that makes them invisible also renders there surfaces unhitable.
As to get to the rest of the ship there are lots of visually hidden lifts in the smuggler ship. They function the same as any other lift just you can't see the red floor tiles due to walls.
You know what? I've successfully killed a bunch of these guys, and it never once occurred to me to use an aye phone to find them. That makes me feel stupid. (I also didn't use grenades.)
As it turns out, there is one angle from which you can see & attack the stargods. If you can work out where they are (eg, blocked terrain), then walk around that spot until you find the right angle - then kill it! (Note: you have to be on that same angle to actually shoot it too. Knowing where it is isn't enough. You can't hit it from the wrong angle.)
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I guess part of the reason I didn't think to use the aye phone is that I didn't have on the first time I met a stargod, and so I suppose I just worked out how to beat it without the sensors and then stuck with what I knew.
