Trying to find this really cool story I read in an anthology years ago, about a future nanobot augmented humanity that was essentially immortal, travelling around in a spaceship large enough to contain entire solar systems; It takes place over the course of 50,000 years and involves the creation of an entire cult religion from the millenia-spanning subterfuge of one bored societal member.
The main character has kids, who find an object on one of the planets inside on of the systems inside this giant "spacecraft" for lack of a better term. Unknown to anyone, the object was placed there by a member of this future society that was bored with the way things were and wanted power and control; this guy causes the humans to crash-land on a "planet," which is sort of inside a dyson's sphere type thing, and while temporarily stranded there uses this object to make a multi-thousand year cult which, at the very end, the main character (a woman) flies down to hopefully free them from this false religion (that's the end; there is no continuation to tell if she was successful).
One other detail; the humans were SO augented with cybernetics that they are described as being unrecognizable as humans to us; they are described in such a way as to make them seem like Mecha. When they get injured, nanobots repair them in time and they are as good as new.
The work might have been in an Asimov or Nebula anthology, early to mid 2000s perhaps?