This summary was pieced together from all the alien tablets, as kindly recorded by Lifoux and Co. in their comprehensive guide:

https://sp.zhabite.com/sharedfiles/filedetails/?id=630495858

If there's any crucial details I've overlooked, please let me know where you found the relevant tablet and I'll amend this guide. Thank you space cadets!

Note: I hear tell of some later alien texts still to be referenced, but not seen in Lifoux's guide. Time to put on that dented helmet again I guess.

This is what I got:

1. The primitive aliens ('The Primitives' I'll call them) had been nomadic hunter gatherers on their own planet.
   
   
2. Their migrations were guided by distant flares, through an environment undergoing radical changes. Although just who lit the flares, and whether the environmental were natural or not, remains unknown - but the two appear connected.
   
   
3. Some kind of atmospheric or solar event caused an environmental crisis. An advanced race of 'Sky Ones' descended, and transported them to the planet 'Galea', featured in the game. (also known by Humans as Gliese-6143-C).
   
   
4. The Sky Ones built them a stone city and supplied it with power. They also gave the Primitives some tech for shaping stone themselves (with some kind of fiery ice). But most other tech (e.g.vehicles) were not supplied, and remained seemingly miraculous.
   
   
5. The Sky Ones were isolationists, living mostly deep underground in hot volcanic regions When surfacing, they were seen to shoot down visiting spaceships using an energy weapon (a memorial exists to a downed non-human astronaut who found shelter for a while with the Primitives).
   
   
6. Despite there city, the Primitives' life was hard and death rates were high on Galea.
   
   
7. Within a generation the Primitives had split into two factions: Followers and Heretics.
   • The Followers were lead by a small cadre of their priests (the Enlightened). They revered the Sky Ones religiously, and believed the faithlessness of Heretics was the reason why the Sky Ones would not make them their technological equals.
     
   • The Heretics initially just wanted to return home, but their conflicts with the Sky Ones resulted in swift collective executions - for the rebels and their families.
   
   
8. Hoping their faith would be rewarded, the Followers collaborated with the Sky Ones, by recruiting their young to participate in a rite called 'Ascension'. Turns out this rite actually sacrificed the young Primitives in a process to unleash / create a malignant smoke-being from a Ball. The Sky One's used these creatures to power their own technology.
   
   
9. The Heretics staged a revolution and besieged the Followers who sheltered behind locked stone doors.
   
   
10. The Heretics won the siege with the assistance of 'Kur,' the apostate priest and former ambassador to the Sky Ones who had seen first-hand what the 'ascensions' really involved. The surviving Followers fled further underground.

So just who were the aliens piloting the Pyramid in the final scene?

• It couldn't have been the Heretics, since they were violently opposed to the methods used to power the Sky One's tech. We don't see them in-game, so seemingly they have since died out naturally, been exterminated, or perhaps remain somewhere in hiding. Only a memorial to their rebel leader remains for the player to find.
  
  
• It's unlikely the Followers are the pilots, since they never showed any signs of progressing beyond their cargo-cult religiosity. Nor would the Sky Ones have much desire to suddenly empower this race they have deemed so disposable.
  
  
• So that's leaves only the Sky Ones as the Colonists' most plausible welcoming committee. We can only wish them well with all that, in the spirit of inter-species cooperation and understanding!