I did the same as you, I saw no reason to get involved. However, I think it’s a problem of game mechanics, rather than narrative. The problem mechanics wise is that there is no reason to care about individual havens. There are way too many havens to even keep track of them and there are no mechanics that would make any particular haven important to the player. I suggested something in this regard here Diplomacy and base management overhaul proposal (sorry for plugging in).
As to the narrative, I think what happens is entirely predictable and convincing.
The factions hold opposing and irreconciable visions for the future of humanity, this is clear from the start. Coexistence is impossible.
It’s kind of like the Thirty Year War. That ended in the Peace of Westphalia because eventually the warring parties realized that none of them could prevail over the others. Incidentaly, our World Order is still largely that of the PoW, as the European powers exported this coexistence model to the rest of the world during the times of the colonial empires. As convinced Westphalians (after all, it has worked for us for nearly 400 years… It even carried us through the Cold War, which could have well concluded in an extinction event) we view peaceful coexistence as the obvious optimal solution. However, the world of PP is a post-PoW reality, in which coexistence is a very difficult proposition.
All this to say that it’s not that an explanation is need for what happens, rather the opposite is true: something imaginative and radical would be needed to prevent it…