The Silent Crusade is a quest line as well as a feature that was added in the Chaos patch and updated twice more, once during the Alliance Rising patch and again in the Mutiny patch.
If you press(comma), you will bring up the Silent Crusade window by default.
The Silent Crusade quest line becomes available at level 75 when the Subway Worker tells you to come at once. You will receive an item that will teleport you there if you want to do it. At the subway, don't buy a ticket but enter the subway construction site. You will appear on a special map. Talk to the woman there who says her leg hurts and she can't move. Defeat the Black Wing monsters. Talk to her again and enter the portal closest to her to defeat Crimson Rock (a boss). Go back to her and her leg will be fine. Complete the quests and leave through the portal on the far left. Use the item she gave you to go to the Excavation Camp (outside of Perion). Talk to her there and she will tell you to go to the Mysterious Gate further inside of the Excavation Site. Find her, enter the gate, and defeat the Skeleton General inside.
You're now initiated into the Silent Crusade. To continue, you must pursue stronger and stronger corrupted bosses. You can find out which ones you still need to defeat by opening up the Silent Crusade window.
Silent Crusade bosses are as strong as their regular counterparts.