There are a lot of different theories about Pink Diamond and what happened to her. Some believe she was Rose Quartz, some believe she was killed by Rose, some even believe that the fusion on the Crystal Temple is Pink Diamond. Here's my theory:
Pink Diamond was a diamond and part of the Great Diamond Authority. She oversaw of the mass production of gems and kindergartens throughout the Gempire (as evident by the pinkish gems on top of the injectors). Rose was an important quartz in Pink Diamond's court and was responsible in the kindergartens on Earth. She saw firsthand the damage mass production was doing to Earth and rebelled against Homeworld with the Crystal Gems. Pink Diamond supported the rebellion, at first by secretly giving the Crystal Gems resources and information, and later openly commanding rebel gems. Close to the end of the civil war Pink Diamond was assassinated by Homeworld Gems; her physical form damaged, her gem shattered, and the gem shards becoming one of the first gems to be part of the Cluster.
So that's my theory. Comment below what you think about it.