Hello.
Some ideas about endgame content:
After the destruction of the protomolecule base, the research of the "Nanite" technology becomes available. These are nano-robots that selectively destroy the protomolecule on the entire planet (surface).
Research unlocks the "Nanite Capsule" item.
The mission "Planetary Purge" becomes available: launch Nanite Capsule (or 10, for example) in a rocket. After a successful launch, the entire protomolecule (bases, nests, units, etc.) disappears from the planet (surface).
After that, the technology "Home Sweet Home" becomes available, which allows you to create a "Hibernation Pod". By installing this pod in the rocket, you can finally fly home.
Rocket launch with this pod - Victory!

Loved it!!! ;) Will do.
How about space exploration. I have to think something about it. A rocket is required in each planet. I can skip the last part if playing SE, that has its own victory condition

Yes, SE already has interplanetary/intergalactic passenger rockets. Hibernation pod is not needed. Victory condition is to research "Home Sweet Home" tecnology (or its own victory condition).