If you enjoyed the post, and the author's website, be sure to read some of his books too!
They arranged to have the simulation in our universe turned off, but not to have all simulations turned off -- there's no way they could do the latter. So they ended up in a simulation run by someone who'd started off by simulating Earth, and who -- more likely than not -- were especially interested in embedded simulations.
Embedded simulations like theirs, but also like the Autoverse, and whoever it is was interested enough that they'd violate the simulated physics of Earth to keep simulating the cellular automaton despite the physics of Earth saying it should be shut off.
Viewed from that perspective, the ending is... not predictable, exactly, but at least plausible.
Honestly as the other response says, indeed there is a parallel universe part to it.. For which I didn't really understand it relation to "dust".
I also liked "Quarantine" which made Quantum Mechanics somehow more intuitive to me. Truly a great writer.
The other universes count as part of the "dust".
The characters in the book thought it would be only random 'simulations' that accidentally happen sometime in the universe's infinite future that kept running them -- that is, literal dust.
They were wrong. Simulations in entirely disjoint universes also count, and aren't nearly as predictable.
His short stories are also criminally overlooked.
That was exactly my feeling after finishing this novel. I went on to read Diaspora, another excellent book.
I think I was prejudiced against sci-fi because of how it is generally portrayed in movies and TV, with an emphasis in odd sounding words and fantastical themes. But Greg Egan makes a fair connection with the current world and expands it with such credibility, you can definitely see some things happening.
And just that, from a cosmological perspective, the chances of us being hit by a gamma ray burst after the kind of technological advancements described but before the capacity to evacuate or shield biological lifeforms arises is... slim. I figure it was introduced more as a plot device than anything else, the biggest deviation from potential veracity (and a "take that" at anyone questioning said potential veracity, which goes just beyond cheeky to slightly obnoxious).