Maybe in the fanfiction, Flash discovers Peter's identity in a very unexpected way, such as seeing Peter's Spider - Man suit by accident. He then has to decide whether to keep the secret or not. He might struggle with his own jealousy towards Peter and the newfound knowledge. If he decides to keep it a secret, it could lead to an unlikely friendship between them, with Flash helping Peter in small ways without Peter knowing it's him.
Iris remains alive in the Flash comics. The creators have kept her as an important and ongoing presence, and her role continues to evolve and contribute to the overall narrative.
The fanfiction could take a route where Flash becomes Peter's sidekick. He might start training with Peter to be more helpful in fights. This would be a huge change for Flash, from a bully to a helper.
Obviously, Iris and the Flash are the main characters. Iris is the one who is pregnant, and the Flash is her partner, so they will be at the center of the story.