You get a total of 5400 Spirit Crystals when starting the game, which is partly because of the pre-registration rewards. This is enough to perform 2 10-summons in the game.
Login Bonus
There are currently 2 login bonus rewards available. After logging in for 7 days, you'll be able to get 1600 Spirit Crystals.
Quests
You can get 10 Spirit Crystals when you clear Quests and Story modes, as well as some extras when you complete the quest challenges.
Completing a chapter by getting all of the stars of the quests will give a clear reward of Spirit Crystals as well.
Missions
After clearing the first chapter, the "Missions" section will be unlocked. The daily missions give 150 Spirit Crystals after completing them, the regular is for certain milestones achievements. Bingo is a special thing that also gives unique rewards and may contain Spirit Crystals.
Spirit Crystal Shop
You can purchase Spirit Crystals with real money from the in-game shop. There are special packs and regular deals, and buying Spirit Crystals this way gives you some Paid and Free versions of Spirit Crystals.
Paid versions of premium currency often have more value in the game since it's used for something like special banners. There is no specific use for the paid version just yet, but it's recommended to be careful with it.
Character Bonds
In the game's menu, select "Character Bonds".
Each character can reach bond lv. 20, and there are Spirit Crystals at certain levels. Bond level increases the more you use that ally in battle.
Tap on a character and select "Bond Level Rewards" on the bottom left to see their rewards list. Tap the "Collect All" button on the bottom right to quickly get all the rewards you have available.
Most of the characters give about 650 Spirit Crystals at level 20, but some can give 700. The amount may vary with some characters.