In the end Phos is the true villain, eliminating everything that it humanity to be human and cutting off the path to Nirvana for all creatures to come after humans forever. I feel lied to and betrayed at the end of this.
I wouldn't say Phos is the true villain. Humanity is. Phos is just a victim to it.
Phos was tainted by the greed and desires of humanity. Phos was like a baby at the beginning of the story, a fresh new slate with no knowledge of how the world works. But in actuality from the moment Phos was carved into the shape of a human/humanoid, they were already tainted by humanity. Adamant has been tainted by humanity from creation and thereby taints the gems with humanity just by carving them into the shape of humans and telling them about human history.
Unlike Phos, the other gems did not have the innate curious nature that Phos had. Another important note: Curiosity is one of the defining characteristics of being human. As Phos grows more curious and gains more knowledge, they grow closer and closer to becoming a human, which im sure many readers was sensing throughout the story.
Phos' extreme curiosity was also their downfall as they sought to seek the truth about too many things and in the end experienced a full life of loss, grief, joy, and anger. The moment Phos had a desire to become stronger and make more friends and figure out the whole secret with the war with lunarians, they were already doomed, because having desires is what brought humanity to its destruction.
On a whole other side note, lunarians are also the remnants of humanity, but the greedy and dishonest part of it. When Phos finally meets them, Phos was already in a deteriorating headspace, stuck between thinking gems were good, Adamant was bad, lunarians good, or Adamant good and gems good and lunarians bad, etc.
As Phos descends into chaos and self destruction, they somehow finally become a true human, which makes the metaphorical meaning of being a human kind of sad but true as well.
And by the tricky of the lunarians, Phos was also tricked into becoming a God. When Phos awakens from their new form, their resentment causes them to wish/pray everyone away, but it leaves them entirely alone, which Phos comes to realize was never what they truly wanted.
Just like a human, in a fit of rage we sometimes do something horrible we didn't mean too, like mudering a loved one out of anger but soonafter coming to realize that they're now gone forever and we will never get to speak, see, or enjoy their comfort ever again.
So, in my opinion, i don't think Phos was ever the true villain. It was humanity. The spirit of humanity is what made Phos destroy everything. The remnants of humanity made Phos human (too human in fact) and allowed Phos a deeper sense of sentience. Someimes it is said that too much knowledge is a curse and that is basically what happens to Phos. They discovered too much, learned too much, realized too much and in the end destroyed it all because their human emotions was too much.
I think that's why after the destruction of everything, Phos begins speaking in a weird monotone and lack-of-emotion way because they're rejecting the humanity in them that made them destroy everything they loved. They hate humanity for what its made them into.
Obviously as humans, its kind of frustrating to read a story that makes humans seem so irredeemably terrible (i mean we are terrible ngl), but in a critical POV, its also important to understand the intricacies of the human spirit and all it's destructive aspects as well.
Whose to say the little rocks on paradise planet won't be tainted by humanity or just the idea of it and turn into destructive little creatures in the future. Is desire strictly a human trait or is it actually a trait of sentience? If the little rocks are sentient beings, what's stopping one little rock into growing curious and following into Phos' footsteps to discover more about their life and the world they inhabit.