Based of the Potter Fact:
142. Severus' boggart was not Lily's body- it was Harry's. He resigned himself to Lily's death, but he could not have handled Harry's death, because he was his last connection to her.
Fearing the Truth
Severus Snape brushed past the group of third years who all were standing flocked around that werewolf with admiration shining in their eyes. He grimaced at Neville's face as a snide comment about the boys ineptness at anything remotely magically tumbled from his lips. If the Dark Lord had chosen him rather than Harry, Lily would be alive. Lily would be here, and even if she hated him still, there would be blood running through her veins and a smile on her face somewhere in the world.
Devoured by his thoughts he got up one floor of stairs before realizing his lesson plans were lying on the table in the staffroom. While he had no desire to head back, he need them to check that he had all of the proper supplies for the potions. Sighing, he headed back toward the classroom occupied by Lupin.
His face twisted into an angry sneer as the door opened to reveal Neville standing smiling in front of a carbon copy of himself that had been forced into woman's clothing. Silence fell across the room as he entered and the boggart morphed back into what Snape looked like in his natural bat-like state. "I forgot my lesson plan," he seethed as he stormed in front of Longbottom.
"Severus," Lupin started making Snape stop, something he deeply regretted afterward. There was collective gasp as the boggart channeled in on the Potions Master and suddenly Harry Potter was lying on the ground a trickle of blood seeping from his mouth. His eyes, so like Lily's, were frosted over in death.
He stormed away from the boggart and grabbed his papers and pushed his way past Ms. Granger who was gripping her friend in mortification. Had he not wanted desperately to get away from that room he'd have stopped to bask in the glory of the dumbstruck look on Weasley's face.
Once he was in the hallway the door opened again to reveal Remus who was watching him with appraising eyes. "That's why Albus trusts you, you're protecting the boy."
"My relationship with the Headmaster is of little concern to you," Severus seethed.
Remus didn't relent. "Why, Severus? You put all your efforts into hating him. You see him as nothing more than his father, a man you hate, a man you have the right to hate. Why?"
Snape's lip curled as he stared at Lupin. "Why?" his voice wavered. "Why? He is hers as much as he is his. He is all that is left of her in this world. I let her down so many times. I wasn't what she wanted. I was stupid and childish, and she moved on from our friendship. This is the last thing I can do to make up for saying what I said," his voice was angry and bitter as he admitted his love. Severus Snape could not quite tell himself why he admitted this to Lupin. Master Moony was part of the Marauders, part of the group of people that snapped his temper and made him say the unforgivable word.
"Lily?" Remus asked in a soft voice.
That was why. Remus knew what it felt like to never be able to be with someone. The only difference was that Lupin could never be with anyone for far more noble reasons. "Expecto Patronum." Snape began to walk away leaving his colleague to stand in the light cast off by the doe.
"Class dismissed. If I find any of you have gone gossiping about what you just witnessed from Professor Snape, I will be quite disappointed in you," Remus' words came out sharp and they floated down the hallway to Severus.
"Always," he whispered as he looked back and the doe vanished.