Lily meets with Severus just before her wedding to James. Several months after the wedding she, already pregnant with Harry, confides in him that James is abusing and or cheating on her.
possibilites:
Lily and Harry survive the Halloween attack, and Severus helps them go into hiding. They live as a muggle family until 'things happen' and they can no longer hide the truth.
or, darker:
Snape kidnaps Lily and hold her hostage. James comes to rescue her, and Severus either tortures him or they run off together. or both.