At the center of the Crystal Hollows (approx. 500x 500z), you will find the Crystal Nucleus. In the Crystal nucleus, you will see 5 statues with their hands out, and when you walk up to them, you will see text that says they need a crystal of a certain gemstone. Getting all of the gemstones will unlock rare loot chests, which are still unknown what they are right now. All structures in the Crystal Hollows spawn randomly in their respective areas, so coords cannot be provided.
This quest can be done multiple times to receive the rewards again.
For the sapphire crystal, you are going to want to go over to the sapphire mines and find Professor Robot. He can be found in a big open area that looks like a ruined city.
When you talk to Professor Robot he will tell you that you have to retrieve all of the parts to rebuild the Automaton Prime.
These parts are rare drops from the Automatons, iron golem like creatures found all around the sapphire mines.
There are 6 unique parts that you have to bring Professor Robot - the Electron Transmitter, FTX 3070, Robotron Reflector, Superlite Motor, Control Switch, and Synthetic Heart.
Once you give all of the parts to Professor Robot, the body of the Automaton Prime will open, where you can walk inside and find the Sapphire Crystal
For the Jade crystal, you need to go over to the Mithril Deposits, and find the room with the gold block floor. above the floor, you will find a walkway with 4 different NPCs in each cardinal direction, when you talk to one of them, they will give you a Metal Detector, which when held will lead you to the nearest treasure.
You need to talk to each NPC and they will tell you that they need a different item corresponding to they type of mineral they are (i.e. the diamond guy wants a Scavenged Diamond Hammer). The treasure can be found on the gold floor of the room and can only be found by holding the metal detector.
When you hold the metal detector it will start making noteblock sounds, and as you get closer to the treasure, it will start getting faster and the pitch will get higher. When you get close enough to the treasure, a chest will appear and which you can click to get the reward. The reward will be powder, gemstones, or one of the quest items needed to give to the NPCs. Once you give each NPC the item they need they, the Jade Crystal will spawn in the middle of the room.
For the Amethyst Crystal, you are going to want to go to the jungle, and find the jungle temple.
To get into the temple, you will need at temple key, which can be obtained by killing a key guardian, or by buying one from the village for 500 sludge.
Being in the big area around the temple nulls out any potion affects, and they will resume when you leave the area. The temple is a parkour challenge, and since you have no potion effects, you don't have jump boost or speed, so using a black cat pet for speed is ideal. The parkour is full of traps and lava, and if you die or touch the lava, you get teleported out of the temple and you will need a new key to try again. Reaching the end of the temple will reward you with the Amethyst Crystal
For the Amber Crystal, you need to go to the goblin area and find the goblin queen.
There are some guards guarding the queen, and you have to get in to get the crystal. You need the King's Scent potion effect to get past them, which I just got from drinking a God Potion.
The crystal is just sitting in the middle of the room
The Topaz Crystal is gotten from killing the Bal boss in the Magma Fields.
The amount of health it has is unknown, as the nametag on the boss says BOSS Bal ???. After doing some damage to it, it will drop a bal pet, and you will want to equip this asap since it gives immunity to the heat effect that you get in the Magma fields.
When enough damage is done, the boss will teleport to the middle of the arena and shrink down until it is gone. The crystal will spawn floating above
When you complete the quest, you will receive some rewards that spawn by the portal looking thing
The rewards consist of various gemstones and some other items