In Aria, the Martians were able to stay on good terms with Earth so they could put all their resources into terraforming as intended and went a little bit overboard: Mars has now a breathable atmosphere, but is also under water!
As in the WMG above, Mars stayed on good terms with Earth, completed the terraforming project and became a bridge to the Belt, as well (just look at the haircuts of Gus and his ex, how cosmopolitan Mars is and their Texan colonists).
- The protomolecule masters aren't dead, but actually either went off to another dimension or "ascended" to a "higher plane of existance".
- There was no "unknown aggressors": The "bullets" are actually safety mechanisms against the abuse of their technology (e.g. the shit the Duarte pulled) left behind by the protomolecule masters themselves.
- The protomolecule was eventually tamed enough that the humans who colonized the new System far from Sol used it for their otherwise unexplained Artificial Gravity. Blue Sun is almost certainly descended from Mao's company. The PAX might also have been developed based on knowledge of the protomolecule.
- Since the weapon is cultivated from human bodies, the more dead bodies that arise, the better - and a war provides a very handy source of them. They don't really care who wins as long as they can reap huge profits after the fact.
- Eros in particular meets their criteria. It's explicitly a crossroads, with representatives of Earth, Mars, and the Belt available in quantity. With a resident population of 1.5 million in addition to the transient population, a broad cross-section of humanity (all ages, genders, racial phenotypes, etc.) is available to study how the weapon interacts with a variety of subjects. And the asteroid is easy to isolate, meaning that the spread of the weapon can be contained while it's studied.
- Its heavily implied that the space station behind the gate is a hub, and the rest of the recently opened gates were already established. However, theres no contact with any non-human traffic going in and out any of the other gates.
- The protomolecule was created by a race that wasn't at the top of the food chain. As, more or less, a simple construction vehicle, it curb-stomped everything in its path.
- Mankind might have been spared the destruction because the gate in its solar system failed to form until significantly later in the universes timeline.
- Human colonists will find more alien ruins, and pick through them until they alert another empire.
- Confirmed in the books.