Starbound mod

------
    If we're gonna be talking about better stories than vanilla..

    >Finish gathering all the bullshit.
    >Return for battle against the ruin.
    >You fail. It turns out the creature was one of many millions, all of whom now begin to pour out of the Gate.
    >Esther is killed horribly.
    >You have to save your companions from the Ruin but its incredibly hard to save them all, you'll probably manage 3 at most.
    >The cultivator was a lie theorized by hopefuls who wanted a universe that wasn't merely prey for powerful otherdimensional entities.
    >Nox dies horribly after trying to control the Ruin.
    >You and your friends escape.
    ...
    >The Ruin and its kind sail the void between planets, seeding worlds with spores that turn planets into tentacle and flesh biomes, killing all native life.
    >Day by day more planets are lost. This portion of the game is just about fleeing from the Ruin and trying to scavenge the resources needed to survive, picking up whoever you find on the way.
    >Eventually the creatures spread themselves thin. As they expand from ground zero, they make mistakes, passing by solar solar systems without consuming them.
    >Islands of safety, comprising of those few lucky star systems untouched by Ruin, dot the galaxy, ports of call for anyone who survived. Most of the planet-sized Ruin entities have left civilized space, no doubt to prey on the vast, endless universe arrayed before them, leaving eldritch worlds of flesh and blood in their wake.
    ...
    Gameplay now becomes more difficult as endgame-level tentacle worlds comprise over 70% of all planets, making gathering resources difficult.

    The enclave systems that survived now fight amongst themselves for pure worlds untouched by the Ruin. Planets are taken and retaken, empires form and fall, and occasionally a wandering Ruin creature attempts to prey on an enclave, with varying chances of success. You can travel between the enclaves as a trader, join them as a soldier, or even carve out your own territory.
------
Also I didn't have enough space to type it out but I also had an idea for a reeeaallly long quest chain where you created a bioweapon that may also have occult otherdimensional energy infused in it, and use it to wipe out the ruin. All tentacle biomes become barren worlds, devoid of life.
-----
My idea would be that all the companions can be saved, and you choose which order to try and save them, right? Buuut the missions to save them get progressively harder the more you complete, and you only have one shot at each.
----
Alternate end:
Have you kill the Ruin, the crone betrays you and attacks you by surprise, and while you're prone and wounded begins monologuing over you about how she'll remake the protectorate in her image.

THEN the other ruin-beasts begin to pour forth, something the crone didn't foresee or contemplate, because she bought the creator/adversary story.