Mods must be activated in-game using the mod selection menu to take effect. To activate mods, open the mod selection menu from New Game or Continue using the "Mods" button shown at the bottom-right of the screen. Enabled mods are then tied to save data and are automatically enabled when save data is loaded.

Mod Pack 2 contains the following mods:
- Passive Trainer: Adds three new NPCs around the world each teaching passives for a cost.
- Doge Shield: Adds a shield that triggers a counter when you're attacked, similar to the Duelling Shield.
- Equipment Expansion: Adds more equipment to Crystal Project, ranging throughout the entire game. Many new chests to find!
- Moonlight Project Custom Classes: Adds four custom classes. Their masters have been spread across the world.
- Bloodmage: A magical class focusing on Mind and that can use HP for buffs and debuffs.
- Additional Boss, Yasha Tar: Adds an additional boss and a new piece of equipment.
- Additional Boss, Pinga: Adds an additional boss and a new piece of equipment.
- Tempest: A physical class focusing on Agility and Mind.
- Forcemage: A magic-using class focusing on Spirit that is capable of being a tank, support or damage-dealer.
- Barbarian: A physical class focusing on Vitality and high HP that is capable of being a tank, support or damage-dealer.
- Additional Boss, Quintar Husk: Adds an additional boss.
- Additional Boss, Elder Entities: Adds an additional boss and a new piece of equipment.