The Brotherhood lost the Siphon after the Darkness escaped from it, so they vanished for a long time. Since The Brotherhood is unable to cover the world in darkness without the Siphon, they decided to burn the world with light, so they built the Prism of the Brothers and waited for the Angelus and the Darkness. When they reemerged during WWII, The Brotherhood supposedly managed to defeat the Angelus and seal her inside the Prism, where she is said to remain to this day.
A terrified Johnny Powell reveals that the Angelus isn't actually trapped in the Prism. In fact, she never even touched it. He always thought she'd disappeared during the war because she was in the Prism, but she wasn't, which begged the question, "Where the fuck is she?".