This is pure fiction and will not follow the Mythology we all used to know, read, or acknowledge.
The story setting will be in the modern world, where god and goddesses from ancient time walking around humans.
In the mythology, Athena was known as Parthenos (Παρθένος "virgin"), because, like her fellow goddesses Artemis and Hestia, she was believed to remain perpetually a virgin. She has no male companion, as to avoid having a fate similar to her mother, Metis.
But in this story, Medusa was her lover. Before she banished Medusa away from her home.
Reader discretion is advised, some of you may find the story isn't up to your taste. And that's okay.