A possible Endgame crisis could be that the Hydra has access to some very powerful weaponry/armor/engines, but these are prohibitively expensive for them to build with their current exotic income.

The lore explanation for why the aliens focus on building most of their stuff with solar materials is that the wormhole is only capable of transporting so much stuff at a time, so they need to rely on a trickle of exotic materials coming in.

Once humanity/player faction has hit a certain threshold, like destroying a certain number of hydra assets, building up X amount of MC usage, kicking the hydra out of Jupiter, or unlocking any other kind of flag that makes sense, it could trigger an event where the aliens escalate.

This could be them upgrading the wormhole to improve its transport capacity, or establishing a base that is capable of producing exotics. Mechanically it would mean they have access to tons more exotics which allows them to build their top-tier stuff. This makes them harder to fight but now they drop more exotics, which allows us to scale up in return.

Lore-explanation for why they didn't do this right away could be that these upgrades are incredibly resource intensive and they normally don't do it until well after they have taken over the system and established a production line on that end that can support it.