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Severus could not deny the timing, and he could not deny one of the most basic, well-studied magical functions. Harry was conceived thirty-eight weeks and two days before the wedding - Lily was with Severus that day and that night and for the day after that and the evening before it. There was no doubt that Harry was biologically his child. How many others had done the math? Had James caught on? If he knew it wasn't his, did he know who else the child could belong to?
Perhaps Severus did not owe Lily anything, but he did start to believe that he owed Harry something. He would do as Lily wanted - he would extend his influence and try to get Harry to find something better in his life.

Lily had never before admitted that Harry did not belong to James. It was something that left her feeling shaken, and she was clearly distracted on her way out of Hogwarts. Luckily, she would receive some guidance from an old mentor.
As she neared one of the floos out of Hogwarts, she heard an old, familiar voice call her name.
"Miss Evans! Ah, I'm sorry. It's Mrs. Potter now, isn't it? It's wonderful to see you."
She turned to see the owner of that friendly voice and to greet her in turn. "Professor McGonagall. It's wonderful to see you as well." She feigned a smile.
"I heard you were here to see Severus. You look like you need someone to talk to."
Her eyes welled up a bit and she nodded. "You know, I really could."
McGonagall took them to her apartment and brewed the two of them some tea. "I can't imagine what must have brought you to see him after all these years. Is everything all right?"
She sifted through her thoughts. "No. Professor,"
McGonagall interrupted her. "Minerva, please."
Lily nodded, although it made her uncomfortable. "Minerva. Are you familiar with divorce?"
She looked over the younger woman gravely. It had been a very long time since she had heard something so sad. "Oh dear. Yes, I'm familiar. Is it really so serious?"
Lily shook her head. "I don't know. I was the most promising witch this school had seen in decades, Minerva. I could have done anything with my life, and I promised it to James Potter. And then I spent it raising a son, with the intention of working as soon as he went off to Hogwarts but..." she hesitated.
"Aren't you working now?"
"I suppose I am, technically. But I wasn't supposed to just have a job. I was supposed to be forging my own path. I was supposed to be a great witch."
Minerva took a moment to reflect. "I never knew Lily Evans to be held back from being a great witch."
"That's just it. As long as I'm with him, I will never be allowed to be a great witch. He was supposed to be a great wizard, but he can't be a man long enough to do anything with himself and so every bit of progress I make he just works to undo me."
She took more time to reflect - this was not something she or anyone could say lightly. "I mean what I said. The world cannot afford for you to be held back, especially not by your own husband. It's bad for the war, it's bad for women, it's clearly bad for Harry, and it's bad for you."
Lily let out a deep sigh and nodded. Minerva confirmed things she already knew. "I don't know how to do it. Divorce doesn't exist here."
"It is very complicated, but you need to be straightforward about it. Renounce your marriage, make it clear to everyone that your marriage no longer stands, and do your best to come to an understanding about your property and your child. Emulate the Muggle system, I suppose."
"I'll have no friends left..."
"I highly doubt that. You have many people that love you."
"But I will be the deserter."
"But you will still be Lily Evans."
She smiled. "Yes, I suppose I will be."