Some of the basic info is this does happen and occurr completely different from the manga and anime episodes. Also this is also my idea please don't steal.

They are still gems but each person is a pirate and holds a certain position on the ship depending on their current position in the manga.

Examples: Rutile is the doctor, Jade is the navigation, Kongo is the captain.

Phos is also slowly turning good.

The police or rather the lunarians keep trying to stop the gems but they keep losing battles. Phos got captured and convinced to try to turn and stop the other gems from committing more crimes.

Phos was slowly able to convince some of the other gems to join him on the good side aka the lunarians side.

The rest of the crew who Phos didn't try to convince or really talk to when he snuck back on, now think he's a traitor except Cinnabar. Cinnabar knows Phos true intentions were to help everyone not get thrown in jail.

Cinnabar is on the same ship and does talk to the others but feels as if they do not care for him and he hides away. Also they have a main base where some gems stay if they don't wish to go out to sea at that very moment.

I now have made two houseki no kuni aus.

~Ghoulex