Mining is the main source of 'Enchant Stones' and 'Upgrade Crystals'. Here are their uses:
Enchant Stones - used as a catalyst by the Enchanter at Hyrule to enchant special effects into your equipments.
Upgrade Crystal - used as a main catalyst for Reforging and Expert Reforging at the Quest Area
Iridium Alloy Ingot - used as a material for refining your equipments. This will have the same success rate as Phracon/Emveretarcon/Oridecon/Elunium but this will protect your item from breaking
To start, click on any Warp Crystal and warp to Mining Area. Use a Merchant-Class Character and talk to Mining Supplies NPC to buy your mining equipments.
You'll be able to buy these gears for 1,000,000z. Take note that these gears are character-bound.
Note: Miner's Pickaxe is heave, expect your ASPD to be drastically lowered. Although you can always equip any other ASPD/AGI gears to lessen this effect.
When you're all set, you can enter this portal to warp inside the Crystal Mines.
You can start mining by hitting any Ore Vein.
You will get a random 'Geode' every 5 hits on the Ore Vein (or a stone, if you're not lucky). From here on out you can just leave your character while mining, alt+tab, and do other stuff.
Tip: to maximize your time for farming, you can use 3 accounts. One for afk fishing, one for afk mining, and one active account for hunting MVPs. You can also do 2 fishers, or 2 miners, whatever suits you.
Here are the types of 'Geodes' that you can get:
Ordered from most rare(top) to most common(bottom).
Inside the mines, you'll notice these Geode Breaker NPCs. Click these NPCs to automatically break Geodes from your inventory one by one, 1 second per Geode so be patient.
After breaking, you'll get Upgrade Crystals, Enchant Stones, or Iridium Alloy Ingot. Enchant Stone rarity depends on the rarity of the Geode. The higher the geode's rarity, the higher the chance for you to get rare enchant stones.