Desecration is activated when you activate Hardmode Altars during a run. After fighting the Starchild that dwells within it, a level of Desecration is activated on the next layer.
There are three Altars that can be found in the first layer of the first three worlds you enter, maxing Desecration levels up to 3. With each level of Desecration, enemy bullet patterns change, providing a more challenging experience, should you choose.
Beating the game at maximum Desecration earns you Skeleton King, an unlockable character.
Desecration only occurs in Normal mode, where Hardmode Altars can be found.