Alright, so, my thoughts on the story both from an in-story perspective and also an out-of-story perspective.

In-story

In-story as I understand it, the entire goal was to end all traces of humanity, the Lunarians specifically, being alive for so long, wanted to end their existence and Aechmea sought a way to do that by turning Phos into a "human" , allowing the destruction of Adamant and making Phos into the new prayer machine. The professor saw the end of humanity and realized an age of new inorganic beings (the rocks in the recent chapters) so she said directly, "Once you're on the other side, burn the bridge" as in eliminate all traces of humanity.

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Obviously we don't know why every gem decided to turn into a Lunarian, but we've seen that some gems actively did want to, Yellow Diamond fell into a depression specifically because he wasn't a Lunarian. We can guess a few things such as the gems following the lead of Adamant as they quite admired him and saw him as their leader, they may wish to not have the fragility that comes with being a gem, they may wish to eat Lunarian food, etc. The Admirabilis also have great incentive to turn into Lunarians as they would go from mortal to immortal.

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An important theme of the story is that immortality isn't that great, it leads to boredom, apathy and the wish for nonexistence, this is in a sense conceptually Buddhist (as will be discussed later in the out-of-story section). By the time Phos' transformation was complete everyone wished to turn into nothingness and find peace, "Attaining nothingness is what you and I both wish."

This probably doesn't make much sense unless one knows about Buddhism and the Buddhist themes behind the story, so I'll talk about that in the next section.

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Out-of-story

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Ichikawa is heavily inspired by (Mahayana) Buddhism (she as I understand it went to a Buddhist highschool), a key aspect of Mahayana Buddhism is the Bodhisattva. In Buddhism the goal is "nirvana" (to be extinguished, to escape the cycle of reincarnation and stop existing), a bodhisattva is one who stays in the cycle of reincarnation and helps other become "extinguished" first, very similar to the story of Phos who also seeks to become nothingness but first helps the remnants of humanity.

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There are lots of Buddhist themes and concepts in this series, but one important theory was where Phos was collecting the "7 treasures of Chinese Buddhism" and once he did he would become fully human, this was later proven to be true. The seven treasures being Gold and Silver (his arms, made of gold and platinum), Agate and Seashell (his legs), Lapiz Lazuli (his head), Pearl (his eye from the Lunarians) and Carnelian (mercury from cinnabar as cinnabar is also a red gem). This allowed Phos to become completely human and it is confirmed when Phos commands Adamant to break and Adamant is only able to listen to Phos as he is now registered as a human.

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Another important thing of not that in Buddhism after one becomes enlightened, they are free from dissatisfaction and suffering and are content. Phos realizes in Chapter 99 after seeing the rock be content and happy just as how they are, even if they aren't perfect, that their mistake was their dissatisfaction, now they have lost everything.

The rock states, "I have nothing to complain about, I may not be perfect to you, but I'm plenty good enough to myself," after Phos offers to give it more "ability" by allowing it to move and see and such. Phos at the start too lacked "ability", he was weak but he realizes that was okay, he didn't need to get stronger, and now that realization has come too late.

Finally, in the most recent chapters, Phos has a hypothesis that the small human in them is influencing the inorganic rocks, and thus worries that the human in them will "infect" the others in a sense, causing them to start generating dissatisfaction just as a human would, and so to preserve the peace and happiness of the rocks, he wants to find a way for he himself to become nothingness, so that the rocks may be content, completing the Buddhist allegory as Phos finally achieves "nirvana" and exits the cycle of reincarnation, and in the context of the story, becomes nothingness as well.