The Prime Kindergarten is a vast, foggy canyon with numerous holes carved out of the dark, dull purple rock faces; which are the "birthplaces" of many Gems. Injectors dot the landscape, some of which have fallen to the ground and been destroyed. The site has a single Warp Pad, which is decoratively surrounded by gems similar to those on the Injectors. This was the first Kindergarten to be developed on Earth and has significantly better conditions than the Beta Kindergarten.
The Prime Kindergarten was once a thriving Kindergarten containing rich minerals perfect for growing new Gems, specifically those of the Quartz variety. However, due to the Rebellion, this facility was shut down.
Once Earth was deemed unsuitable as a colony, Homeworld Gems began their project to create a massive Gem geo-weapon known as the Cluster. While it was not inserted into the mantle through the Prime Kindergarten, a vast amount of prototypes were left here to eventually emerge thousands of years later.
Underneath ground level is the Prime Kindergarten Control Room which has the ability to reactivate the facility, check on all equipment, and access the Cluster prototypes. While the rest of the facility is broken down, this room remained untouched due to the Crystal Gems having no prior knowledge of its existence.
Some of the surviving Quartzes produced in the Prime Kindergarten were stationed at Pink Diamond's Zoo, with the jobs of guarding and maintaining the facility under the command of Holly Blue Agate and Blue Diamond. Each of these Quartzes share the same cheerful, jokester, and casual personality that Amethyst has, which might be because they all came from the same planet.
Amethyst introduces Steven to this location. She reveals that she was made there and that Gems used this place to create other "bad" Gems, or "parasites".
The Crystal Gems follow one of Peridot's Plug Robonoids here. They later cut Peridot's connection to the control room, at the cost of her discovering their existence of on Earth. Pearl mentions the Kindergarten has been inactive for 6,000 years and would destroy all life on Earth if reactivated.
The Crystal Gems go to the Kindergarten to search for Peridot. They find her, but she quickly escapes. Upon further investigation, Garnet discovers that Peridot wasn't trying to reactivate it, but instead she is checking on Cluster Gems, former Crystal Gems that Gem Homeworld shattered and forced to fuse, possibly as punishment for the Rebellion.
Peridot shows Steven to the Kindergarten to give him more information about the Cluster, as well as referring to it as the "Prime" Kindergarten. She assumes, since he is a Quartz, he is made there as well, only to learn about his hybrid status instead.
Peridot, Amethyst, and Steven retrieve a drill head from one of the Injectors to use on their drill to the Cluster. Peridot also tells Amethyst about quartz and classifies her as a defective quartz.
Buddy Buddwick begins to explore the marked areas Pearl had marked for him to stay away from, starting at the Sky Spire, the Lunar Sea Spire, the Communication Hub, and then the Kindergarten. He draws down the holes made from formed gems, and names the place, "The Many Hole'd Place" in his journal. Buddy feels a bit "off" about his journey until Amethyst comes onto the scene behind Buddwick. He shows Amethyst his accomplishments on the map, journeying to places unseen. However, from the looks of the Kindergarten, many people have been here, and since Amethyst's compatriots drew his map, he comes to realize he is merely a tourist rather than an explorer and adventurer and weeps over it. Amethyst suggest discovering the "Sand Castle" located in the arid environment known as The Desert. This brings back Buddwick's enthusiasm and begins his travel to the Sand Castle.
Holly Blue Agate tells Sapphire and the Gems to excuse the Amethyst guards at Pink Diamond's Zoo because they were made on Earth.
Amethyst reveals that each of the Quartzes stationed at Pink Diamond's Zoo were either made from the Prime or Beta Kindergarten on Earth.
Steven and Amethyst take Peridot to the Prime Kindergarten to cheer her up. At the Kindergarten, Peridot reveals the designation order of the Gems made there after Amethyst incorrectly guesses the exit holes of her fellow Amethysts. The trio are later surprised to discover a lone flower growing at the site. To test the possibility that the Kindergarten has become capable at supporting life, they decide to plant sunflowers, all of which die the following day. With Lapis' recent departure from Earth, their failure to reinstitute life in the Kindergarten pushes Peridot to anger. She exclaims the irreversible nature of her situation, and furiously stomps on the flower they saw earlier. This provokes the Flower Monster, who is quickly defeated by Smoky Quartz. Afterward, the Crystal Gems leave the Kindergarten, concluding that the location is truly dead forever, but taking comfort in the fact that Earth is still full of life.
- The area was stricken barren of life by the incubated Gems around 6,000 years ago, as stated by Pearl in "Marble Madness".
- It is unknown how many Gems were grown in the Kindergarten, and where most of them currently are.
- Amethyst was grown at the Prime Kindergarten but joined the Crystal Gems sometime after the Rebellion.
- Amethyst's hole is one of the few holes at ground level.