Been playing The Last Federation a bit recently...and I particularly like the interactions between the races. How events on one might cause another to attack them (opportunity!) or cause some political problems (Thoraxians in the Federation). Occurred to me there are a few...events that would somewhat fit AIW2 - I've just put a few below.
A note is the Dyson Antagoniser/Converter/Annihilator was somewhat something like this. The Nemesis could possibly even have unique versions of these...once he's in.
Dyson Sphere and Nanocaust
If the Nanocaust hold a planet within a certain radius of a Dyson Sphere, the Sphere has a chance occasionally to become very concerned and focus the Nanocaust with almost everything it has, due to how terrifying being infected by it would be.
Dyson Sphere and Dark Spire
Lorewise this probably isn't a thing anymore, and is only mentioned here, but in Classic the Zenith Devestator noted an ancient war between the Zenith and Spire. For this event, if the Dark Spire are in sufficient strength near a Sphere, they may focus on attacking toward it due to ancient hatred of the Zenith. Of course, they can't actually destroy it, but they'd keep it out of action more or less.
Marauders and Nanocaust
Marauders are just normal humans, more or less. What the Nanocaust would do to them would probably be so terrifying that they'd be reluctant to do offensive actions on them unless they have massively overwhelming firepower. Maybe they'd even pack up a planet and leave (adds to budget somewhere like the Resistance Fighters warping out) if they happen to be isolated and near the Nanocaust.
AI Overlord and Nanocaust
While the AI Overlord might...not be a living thing, being subverted by the Nanocaust would, like above, be generally terrifying that it makes some sense for it to have a much more violent reaction against it being near. Essentially, like Strategic Reserve, but it only ever fights the Nanocaust (it absolutely will not divert this force to anything else - it would rather get blown up than captured).
AI and Player
AI took a leaf out of the Acutians finance book, and decided it's so fed up with the player that it's throwing a moon at their homeworld! Essentially a rare event if Nomads ever return. How you'd stop it I'm not...super sure? Destroy a guidance structure? Effectively the Nomad Beacon done by the AI at you.
Ending
Welp, out of ideas now. This is a...far in future thing, but throwing it up anyway, seeing as factions are a bigger thing now.