Um, this may well be part of BR's reworking of Derelict. I'm going to take it you've played derelict before, so there's a
SPOILER COMING UP!
The Nyarlathotep is dragged out of subspace as a derelict. It is completely inactive. I suspect that the lights only come on after it wakes up, to further scare the crap out of you when the boarding parties go missing. I don't know (I haven't played BR's version) but that sounds like it might be the reason. The lights-on/lights-off sexps would be behind it. :)
EDIT: Added spoiler tags to avoid incurring kietotheworld's wrath.... :p
Oh and pyro, you should use tags, not just put SPOILERS!