After Sirius falls through the veil and Harry goes back to live with the Dursleys, Lupin falls into depression. He turns everyone away, and starts seeing ghosts.
Snape is being pulled further and further into Dumbledore's web, and is finally told that he may have to kill his friend and mentor. He's distracted and doesn't realize that there's anything wrong with the rest of the order until Lupin neglects to pick up his wolfsbane potion.