Shadow cores are the currency used in GemCraft Chapter 2: Chasing Shadows. They can be acquired by defeating monsters, but the main source is Shadows, Spires, Apparitions, and Specters. You receive the aquired Shadow Cores even if you lose the level.
They are used to activate Battle Traits, upgrade Talisman Fragments and to increase Talisman Fragment drop rarity.
In Steam, Battle Traits are free, so Shadow Cores are only used for Fragments.