Complete prompt from the kinkmeme:
Sam wasn't born from the union of Kevin Flynn and Jordan Canas. Instead, he is a program that Flynn and Alan wrote together.
Either they wrote the program at Encom and Flynn brought it to the Grid, curious to meet him, or they intentionally wrote with the intention of creating a kind of offspring. He has all the strengths of Tron and of Clu, of Kevin and of Alan. He could be born fully mature, but I'd love to see Flynn figuring out a way to start him off as an infant and let him develop, and bring him into the real world to raise.
Jordan (or Lora, I guess) could be involved as the "legal mother" because otherwise it might be a bit confusing for them to adopt a kid with no obvious origins. The story could be at any point, when Flynn first brings his child out of the grid, or when Alan finds out that the database he wrote with Flynn is now sitting on his lap, or even when Sam returns to the grid and feels at home for the first time in his life.