Shadow Crystals are pieces of black crystal, with orange highlights and an ornate design. They emit an incredibly high concentration of Twilight in their surrounding area, which causes Hyruleans to lose their physical forms. The Triforce pieces are able to protect their bearers from the effects of the Twilight, but the Triforce of Courage instead turns the bearer into a wolf.
After Link and Midna complete the Lakebed Temple and return to Lanayru Spring, they are ambushed by Zant, who steals the Fused Shadows from them and uses his dark magic to cover the Spring in Twilight. When Wolf Link attacks Zant after he gravely wounds Midna, Zant embeds a Shadow Crystal into Link's forehead, trapping him in wolf form. Link is able to remove the Crystal using the Master Sword, and regain his normal body - afterwards, Midna keeps the Shadow Crystal.
Shadow Crystals can also be evaporated into Dark Fog, a jet-black haze that consumes all light in the surrounding area. Zant uses Dark Fog in order to suppress the Light Spirits and cover Hyrule in Twilight.
In gameplay, Dark Fog is present in all areas of Twilight, but appears as a highly-concentrated, jet-black haze inside the Palace of Twilight. If Link comes into contact with the Dark Fog in the Palace, Midna will automatically use the Shadow Crystal on Link and refuse to turn him back to normal, claiming that the Fog will kill Link if he remains in Hylian form.
A Shadow Crystal appears in the Linkle's Tale scenario "Her True Self". As Midna is returning to the Palace of Twilight to aid Zelda in facing Dark Zant, she runs into Linkle, beholding a Shadow Crystal. Midna is transfixed by the Crystal, and upon touching it, Cia's curse is briefly undone, restoring Midna to her Twili form. At the end of the scenario, Midna destroys the Shadow Crystal to stop the Twilight leaking from the Palace, turning herself back into imp form.
Midna recovers the Shadow Crystal after the Master Sword's power has driven it out of Link.
- Text remaining in the game files suggests Link needed Magic to use the Shadow Crystal before it was removed from the game late in development