Although I posted it in the Tomoyo After Fanart thread first, I’m going to place my fanfic here and update it when I write a new chapter.
https://www.fanfiction.net/s/12138063/1/Letters-To-Papa-A-Tomoyo-After-Fanfic
So far there’s only one chapter up, with four more on the way. I don’t know how many more I’m going to write, if I write any more at all after the Bookclub. Nevertheless, it’s something I can comfortably do while working on my other projects.
Again, Tomo Arc and After Arc spoilers for the uninitiated. Please read Tomoyo After, it’s a great visual novel. And don’t forget to read this afterward! Enjoy~ :3
There’s some supplemental dialogue below with Tomoya and Tomoyo accompanying each letter’s release. Again, After Arc spoilers.
EDIT (09/07/16) - “Oh, another letter? …Who’s Tomo?” 0_o
EDIT (09/09/16) - “Tomoya, this letter is from Tomo, our…our friend.”
“Friend?”
“Yes, please read it. Even though she’s small, she put a great deal of effort into it for you.”
“O-okay…”
EDIT (09/10/16) - “Oh, another letter from this Tomo person…I wonder what she looks like.” ._.
EDIT (09/12/16) - “Tomoyo, what does this Tomo person look like?”
“She’s young and cute. Six years old, I think.”
“Why is a six-year-old writing to me? Don’t tell me it’s because…”
“Whatever perverted things you’re thinking about, it’s not true. Tomo is our friend. That’s all you need to know for now.”
“Uh…sure.” 
EDIT (09/13/16) - “Hey, Tomoyo, what’s a starfish?”
“…You’re joking, right?”
“Yeah, sorry.” ^^;
“I miss Tomo. I really wish I could visit her right now…”
“Then why don’t you?”
“You’re more important right now.”
“Am I really that important to you?”
“You’ll understand soon. I’m sure of it. For now, just keep reading her letters.”
EDIT (09/14/16) - “So many letters…I don’t know where to start. Maybe the most recent will do?”
EDIT (09/15/16) - “Who’s Fuko?”
“…Beats me. I don’t recall seeing any other girls in the village. But it looks like Tomo’s made a friend.”
“Seems so. This Tomo girl really wants me to play with her for some reason. Maybe we should visit her?”
“No, not yet. For now, you need to rest. I’ll go meet Tomo later.”
“Can you give her a message, then?”
“What?”
“Tell her…I’ll be there to play with her soon.”
“…Okay. I’ll tell her.”
“Thank you…”
EDIT (10/15/16) - “This Tomo girl sure has cute handwriting…”
“I know, right? She’s such a cute girl.”
“I wonder if I really am her father, though…I don’t remember ever getting married and having a kid…”
“…”
“…Tomoyo?”
“…It’s nothing.”
“Come on, tell me. Am I really her father?”
“…No, you’re not. But even if she is not your real daughter, you still chose to raise her until her real mother could take care of her again. And those times were very happy.”
“I wonder about that…I would like to meet her sometime soon.”
“You will. We promised we would.”
“Is that so? Then…I look forward to it.”
EDIT (10/18/16) - “Does this kid seriously think General Winter is a person?”
“Hey, don’t make fun of her. It’s like Santa Claus. She’ll learn to grow out of it eventually.”
“Brr…I doubt that…”
“Are you cold? I can turn the temperature up if you want.”
“N-no, I’m fine. This is nothing compared to losing my memories.”
“I can get you something hot to drink later if you need it.”
“Thank you…hopefully I can see Tomo before I catch a cold.”
“…Yeah, hopefully.”
