He got his Lily

[Guest Rock the Boat]

Snape is the first on the scene, and thus able to spirit away the only remaining piece of Lily that faithful night.

or

Snape kidnaps Harry and raises him/her in secret. But not as Harry, but as Lily. Snap raises her child as her replacement, addressing Harry as Lily, forcing the young child to dress and act like Lily, and permanently dying their hair. Hell, might even steal some of Lily’s hair to poly juice the infant. And of course, once ‘Lily’ is old enough, he would be with her.

so, either a fem! Harry, feminized/sissy Harry, or a sex changed Harry. Raised to be the ideal Lily for Snape