The first time Remus Lupin saw his boggart wasn't until after he was bitten. He can't remember what it would have been before and he's not sure it matters. Other days he is absolutely sure it does. He thought it had to be the full moon, because when you're a werewolf that's what happens. You have to do werewolf things, you are afraid of werewolf fears, you live by werewolf rules.
The Defense professor wasn't supposed to let him see a boggart. It was all too common for shape-shifting monsters to turn into full moons in the face of werewolves. Some people considered it a sign. Some people considered it an omen. Some people just screamed.
Later, he'll remember this when he stands in front of Harry. It was less, however, for the class of 13 year olds who shouldn't ever see Lord Voldemort than you would think. Part of it was for him.
Anyway, it was the end of class and no one saw the pale white orb suspended in the air except for the only other second year in the room – watching carefully with his cool grey eyes.
The second time Remus Lupin sees his boggart, it is during his seventh year, before they changed from JamesSiriusRemusPeter to JamesandLily and SiriusRemusPeter. He had friends who loved him, and alcohol that makes it okay to say it and maybe, just maybe, he was finally comfortable, finally happy. On their way to the kitchens however, they run into Peeves, who runs into a broom closet door. When the door popped loose, a boggart came sliding out onto the floor, the pale lifeless bodies of Sirius and James and Peter are tangled in brooms and mops. Remus had been a little ways ahead of them, walking backwards as he told some story, so it was obvious to everyone whose worst fear was the dead bodies of his friends.
(You can't be afraid of what's impossible but four years later he knows there is something worse than their deaths.)
No one quite knows what to do or say so they keep going, James vanquishing the boggart before he thinks anyone has caught a glimpse of bright green eyes, empty and cold.
The last time Remus Lupin sees his boggart, it is after his welcome back to Hogwarts prank. It was simple and kind of sad, but he can't help but laugh as he thinks of the expression on his two (three…always three) best friends faces if they could have seen Snape dressed in Agatha Longbottom's clothes. His boggart then is once again a full moon. But it's different this time, in so many painful, utterly heart wrenching ways. It isn't because he's a werewolf, with werewolf fears, and it isn't because he hates his transformations, docile and calm as they are now. It's because the worst has happened and now there is nothing else left.
(He knows this isn't true. There is Harry, who looks so much like his father. There will be Sirius, who will remind him that it wasn't all awful, that they didn't always have to fake their laughter. There will be Nymphadora and Teddy and the bright light of the end of war. But right then, at that moment, there was only him and a James Potter look-a-like he should have known much better.)