This is a list of possible divergences in the timeline of the story. The list will be chronological, going from early divergences to late ones. Note: this list relies on extragalactic travel being possible, and attainable for societies outside of God-beings. (which I truthfully believe is possible) 

1. What if the Earth-Mars conflict goes much worse? Essentially, what if many more lives were lost, and/or humanity was sent back technologically, possibly for thousands of years. So much so that when the Qu arrived in their migration, humanity was confined to one star system. In the most likely case, humans would be not be mutated to beasts, not having had the chance to destroy alien life. They would simply be destroyed completely, made extinct… But there is a small chance the Qu would spare them. Not to be anything other than another tool— literally. They would be turned into a weapon, much like the biological tracing creature (presumably a different captured alien). In this case, there is no hope of humanity doing anything, being a mindless tool directly controlled by the Qu on their ships. But what if? What if tens of millions of years later, another race defeated the Qu and found these creatures. Looking through their DNA, they recreated Homo sapiens. (Of course this is a completely different universe/story now, of a resurrected humanity waking up amongst an alien society)
2. What if the Qu didn’t exist? This is a much simpler answer. The Star People would continue expanding, eventually colonizing the whole galaxy. They would eventually spread out into the surrounding galaxy, tens of millions of years sooner than in canon. While these grand divides (millions of light years) would inarguably split humanity into a couple different, galaxy-centered cultures, I do not see any particular human galaxy gaining a vast technological lead over another. Nor do I see them waging war on each other. They would continue to work together, under the flag of humanity, always looking towards the next horizon.
3. What if no sapient posthumans evolved? By chance, or by the Qu trying harder, humans are forever reduced to animals (or at least, it would take like 300 million years for one to reevolve a mind). In this case, only the spacers remain— there is no killing them. Space is too vast for the Qu to hunt them all down. As such, they still turn into aloof gods, but this time there is no one to bring them back to reality. In this case, they would probably continue to stew in their self-made worlds forevermore, not devolving, but not quite evolving either. Two things would happen here. **3a.** Eventually, something does change. Maybe a certain individual 70 million years after the Qu leave decides to venture out, and more follow. A society of gods adapting back to men. **3b.** The probably more likely scenario, the Asteromorphs chill for so long that the Amphicephali evolve and colonize the Milky Way. The two would both be very powerful, and they probably would split the galaxy, with the Amphicephali taking the empty planets. Hopefully, the presence of these beings, who truly come in peace, would rouse the Asteromorphs from their slumber to actively participate in this this union. If not, they continue to hold themselves above everyone else and hide away. Eventually, with or without Asteromorph help, the Amphicephali hunt down and subdue the Qu. (Or maybe they fail without help/tech from the Asteromorphs/New Empire?)
4. What if the Gravitals never came about? This would result in an expanded Second Empire. They would exist long enough to colonize the surrounding galaxies (In the original book, the timescale is a bit too large to explain why they didn’t do this already), and thus they can never be at risk of a genocide like OTL. Eventually, probably sooner than OTL due to expanding in less time, they would re-encounter the Qu. Two things happen here: **4a.** They manage to squeeze out a narrow victory. They spend the rest of forever enjoying the wonders of the universe, eventually even growing in power enough to outperform the Asteromorphs, too busy pretending to be above everyone else. The Multi-Galactic Empire of Man leaves the stagnant spacers to themselves in the void. **4b.** The Second Empire in all likelihood was not advanced enough to win— despite colonizing multiple galaxies (or just andromeda depending on how soon the re-encounter was), they did it fast enough that they still lacked gravity manipulation tech, as well as some other advances the New/Third Empire AND the Amphicephali would have had. They would fight valiantly, but the Qu just might come out on top. If they do, they would either completely destroy the posthumans, or devolve them to pond scum, never to think again. In this case, it is possible that the Qu would reverse course, heading back to the Milky Way to try and squash any remaining resistance. It then draws the question of if the Asteromorphs were yet powerful enough to succeed. Frankly, I don’t believe so, and thus this timeline spells the complete destruction of humanity for good at the hands of the Qu. 
5. What if the Ruin Haunters/Gravitals didn’t go insane? Simply put, they are an ally to the posthumans. They join the alliance, and gift the super OP gravity manipulation tech (which I’m 99% sure came from Qu ruins, not Star People ruins). This then becomes a more buffed version of 4. It is still quite possible they loose, but the odds are more even due to the gravity tech.
6. What if the Machine Empire expanded? Truthfully, I believe the Machine Empire had the ability of extragalactic travel OTL, but they didn’t use it due to the entire system being propped up around control (and around Ten if you subscribe to fanon). They chose to remain in one place because they knew another colonized galaxy may become an enemy. But what if they did expand? Three things happen: **6a.** They do indeed divide in ideology and/or new groups want power over the regime. In this case, it is possible that they ignore each other, but they could very well try to war, although at this scale it becomes a lot harder. Probably a lot of shooting quasar beams at each other. I assume they would give up on this endeavor eventually. Possibly even becoming cautious allies? **6b.** They keep a consistent ideology and culture. Eventually, they may even let up on how to treat organics (or just collectively decide to kill them all in order to keep homogeneity). From here it’s hard to say, but they outpace the Asteromorphs due to more resources. They would probably wait until they’re 100% sure, and then kill them. Humanity is again united under one banner, but was it worth it to get here? **6c.** They re-encounter the Qu. This is similar to 5, but possibly even more advanced. Being fully robotic, the Qu’s genetic engineering wouldn’t work on them, but the Qu have other weapons too… It’s a toss up here. Depending on how they play, the Gravitals could win against their enemy, or they could be extinguished. If they did lose, they would give the Qu one hell of a fight. 
7. What if the Machine Empire didn’t attack the Asteromorphs? If they had just left them in the void, the book itself speculates that the Machines may have fallen to Civil War. This would occur here, with the Galaxy-spanning Empire dividing into factions and infighting. In some cases, the infrastructure to support the most advanced tech (gravity manipulation, Dyson swarms, continual self repair) would fail, leading to robotic forms with set lifespans and more animalistic bodies with defined limbs. On the other side, it’s totally possible that intelligent Subjects may be able to take advantage of this power vacuum and lead independent lives— or maybe even kill some downgraded machines! (This is objectively a very cool setting, with factions fighting in the ruins, sort of like space pirates. Also ironically very similar to their Ruin Haunters origins). From here the timeline divides again: **7a.** The fighting gets too extreme (blowing up planets level) and the Asteromorphs intervene, scooping up the remnants and making the New Empire. Despite the Gravitals not being a single empire, they would probably all get turned into the New Machines anyhow, albeit with the memory of this period wiped, so they don’t in-fight while being slaves. Any independent subject factions would probably be destroyed so their children can be raised by Terrestrials free of influence/rebellion. **7b.** Eventually, the fighting simmers. I would assume that the tolerant factions slowly win, leading to a reformed empire/alliance, perhaps called the Machine Republic. The Empire that had to tear itself apart to learn its lesson, but was all the stronger for it. Machines and organics live in peace (mostly because those who try to end this peace are themselves killed). This Machine Republic may remake their situation with the Asteromorphs, as separate entities, but now with mutual respect, and possibly trade. Eventually, the Machine Republic, Asteromorph Empire, and Amphicephali Empire locate and subdue the Qu.
8. What if no organics remained? (Or also I suppose this could be what if Nero was never born, if you subscribe to fanon). Either if there was no life to seed, or no genius to do the seeding. In this case, the Asteromorphs beat the Gravitals, and turn them into slaves, but… then what? This is a society of Gods without citizens to rule over. They have been pulled out of their slumber, but they are not being kept awake by the needs of the many. Maybe they would create new life, organic or robotic, to work as citizens? More likely— they simply send the New Machines directly as workers to populate the worlds. This would probably give them even more stability than in OTL, as they directly altered the brains on the New Machines to be dull and obedient— and what’s more, with no Subjects alive, there is no one to fight for machine rights. They will forever be slaves. The Asteromorphs may not even need to create the Terrestrials, using simpler systems to keep their slaves in line. One interesting thing: without biospheres to protect, and with people able to live anywhere, it is possible that the choose to dismantle many planets to utilize their energy more efficiently. It seems this is a timeline with an even more cold and calculating New Empire than in OTL, focused fully on infrastructure and advancement. They still go on to create the United Galaxies, but, well, everything seems a bit less fun without normal people around. (Normal as as acting curious, spontaneous, and kind, instead of being unknowable gods or submissive slaves). In this timeline, humans live, but humanity dies.
9. What if there were no Amphicephal? By this point in the story, the New Empire is a galaxy spanning beacon of peogress. While not having the alien snakes around would make a less interesting universe, it would not make the Empire that much less powerful— It would still be a bit less powerful, having to colonize this place instead of having the work done for them, and so taking longer. With how restrictive the early New Empire was, it is possible they simply replicate the whole Terrestrial society-raising process again. Or, they actually give their created races a chance to expand, of course under the watchful eyes of their Gods. In this timeline, with no outsider looking in to the system, it is possible that the Asteromorphs are more oppressive than in OTL, since they don’t need to save face to avoid making an enemy. Likewise, the Subjects may be less ambitious, never knowing that more “regular” beings, not zeroed in on achieving godhood, could make a society. Yes, I fully believe that post-second contact, the presence of the Amphicephali would have changed dynamics for the better in the New Empire. This sadly doesn’t happen here.
10. What if the Qu won the final confrontation? I myself don’t see this happening, with how God-like the New Empire was, not to mention partnering with another galaxy spanning empire. But if it did happen, it’s possible that the Qu would try to make everyone extinct, but, much like the initial spacers, many would escape, of all races. In this case, while the New Empire proper was destroyed, many small factions would survive in the void, and, closer in tech level to the Qu, may partake in Guerrilla warfare, slowly depleting the Qu’s resources. Either this, or they simply hide again, until the Qu leave, and try to fight again. Hopefully this time, the millions year long slumber in the void would let them keep their humanity.