From the auther of the story (Wilthywonka) helps clear the ending up a bit: As the deity concluded the conversation with Toveryn, he transported Phoebe through space to the galaxy they were heading to. The hailing ship was another physical race, from that new galaxy, that contacted the lifeship. Toveryn smiled bevause he knew, despite the threat in the message, this was humanity's chance to 'build the city' as the deity described, and spread a galactic community. Another thing, as it was hard to catch, the deity was in fact once a galactic community itself, until it evolved into one non-physical entity. That's why it recognized humanity as special; a race that could cut down the dark forest, build a community, and eventually become something like itself.
The entity chose "SPARE", because humanity had decided to run away, instead of become like the so many cruel hunters. So it allowed humanity to make contact with another race, rather than destroy them.
Ship is going a signifigent portion of the speed of light, and ... they want the ship to ... stop... immediately? Well they are either crazy, or they have tech we don't. Hope that works out.
@@imaginaryparsnip he might have taken it down himself after more than a third of it got demonitized, would need to be done all over at that point anyways.