In the 5th episode of the first season, ‘Frybo’, we are introduced to the concept of gem shards. Pearl says that these shards still have bits of memory and consciousness of what was a complete gem.
In later episodes, specifically in ‘Secret team’ (29th of S01), we see how these gem shards look like when they regenerate. A complete mess of different body parts.
Then in ep. 44, ‘Marble Madness’, Peridot is investigating an abandoned gem facility under The Kindergarten, before the Crystal gems destroy it.
It’s not until ep. 8 of S2, “Keeping it together” when they return there and discover the true horror of this place. In Garnet’s words: “This is punishment for the rebellion!”
What if these experiments were not just retaliation from Homeworld, but shattered them and stuck them back together for a much bigger purpose?
TO REBUILD PINK DIAMOND
This is supported by Blue Diamond’s words referring to the Zoo, the bubbled Quartz stored in Pink’s room and Earth itself: “This is all we have left of her”
Indicating that she doesn’t know where are the remains of her sister, but Yellow does, and maybe together with White Diamond, has kept them in secret and looked for a way to bring her back.
Yellow Diamond’s attitude towards Earth reveals that she doesn’t have to worry about the fate of the planet, even if PD’s shards are still there. Because she has them.
Yellow Diamond doesn’t tell Blue many things, like Peridot’s betrayal, the Rubies’ failed mission and also this, to prevent her more grief. That explains BD secret visit to Earth: “..I shouldn’t be here..” because the other Diamonds told her to never return there.
Y and W Diamond might not have all her pieces, but most of them, explaining why the first gem experiments with captured rebels are shards stuck together, to see if they could compensate with other gem shards the pieces they don’t have.
We all know that those experiments were a failure and are the reason for Yellow’s hate towards Earth and her expectation for the Cluster to rise, to hide her failure of not being able to bring her sister back and her grief seen during her song.
Peridot’s original mission on Earth probably was to recover data from these same experiments because they were ready to try it again, with their new technology and discoveries at Homeworld.
That could also explain why YD send the Rubies to bring Jasper back because she seemed to be the perfect gem to replace PD’s missing pieces or maybe just to assign her to her original Diamond.
This is gonna be a fun like Dragon's Lair style death, where like in a cartoon something happens to you and suddenly it's just skeletons standing there holding the umbrella and the shield, and somebody whistling while they move a lever, because all three of your are almost instantly devoured by something as soon as you leave the light