I've shared this theory before, but it still fits here.
Amethyst is Garnet's daughter.
One of the Crewniverse said that we'd find out if 2 Gems could breed.
I believe we'll find out through a flashback of Ruby and Sapphire.
Ruby and Sapphire saw how humans breed and wanted to try it themselves, but it had the unfortunate side effect of getting one of them pregnant.
Amethyst is established to be the youngest CG other than Steven.
Ruby is red, Sapphire is blue. Red and blue make purple. Purple like Amethyst.
And let's look back at the Sugilite fusion dance. Amethyst jumps into Garnet's crotch. Why? Because it's where she came from. Garnet has those child bearing hips, so Ruby and Sapphire decided to fuse together to give birth to Amethyst.
Speaking of Sugilite, isn't it weird how Amethyst and Garnet have a good relationship, but their fusion seems to embody a bad one? That's because Sugilite is the result on inbreeding.
"But didn't Amethyst come from the Kindergarten?", you may ask. You'd be wrong.
You see, Garnet made the Kindergarten herself as a coverup. There's plenty of evidence of this, too.
In "Keeping it Together", we see the forced fusions. These were made by Garnet to see whether or not Amethyst would turn out okay. They didn't, so Garnet buried Amethyst in one of the holes she dug, shattered the forced fusions, and pretended Homeworld did it. (The fact that Peridot mentions the Cluster in front of Sapphire, but Garnet claims that the Cluster is "new" strengthens this point).
But what Garnet didn't count on was Rose finding the shattered forced fusions and trying to eat them, thinking they were rock candy. But when her saliva healed them, she spit them out because she was a vegan.
Let's go back to "Keeping it Together." Last time Garnet saw the forced fusions, she killed them. Seeing them alive again could only mean one thing: Rose found them and healed them. "Rose couldn't have known". Ruby and Sapphire were trying to reassure each other that Rose didn't know it was them.
This will likely cause conflict when Pearl (Rose's sole confidant) accidentally reveals that she knows the truth, resulting in " Crack the Whip" "Kindergarten Kid" and "Steven vs Amethyst".