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. The Brotherhood managed to defeat The Angelus, sealing her inside the Prism, where she is said to remain to this day.
A terrified Johnny Powell reveals that The Angelus is actually not trapped in the Prism. In fact, she never even touched it.