I Do Not Own Thor or Harry Potter
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It was common belief that the cause of Lily Potter and her sister, Petunia Dursley, split and subsequent estrangement was because Lily was a witch. Since neither sister ever discussed the truth, even with their husbands, it was an easy mistake to make.
No, the truth came out when Lily turned fifteen. It was then that Mark and Emily Evans decided to tell their daughter's the truth.
Years before, after Petunia's birth, Mark and Emily separated. Neither explained why, but they explained that the only reason they didn't divorce was because both their parents frowned upon it. During this year-and-a-half separation, Mark had a…liaison, with another woman.
Who left him after giving birth to Lily. So when Mark and Emily reconciled, Mark had brought his new daughter with him. It was the reason Lily looked so different compared to Petunia. In fact, according to Mark Evans, Lily could pass for a red-headed version of her birth mother.
After discovering this, both girls drifted apart. Petunia saw Lily as the byproduct of her father's affair (never mind that her mother had admitted to sleeping with other men during this time, she just never got pregnant). While Lily, feeling betrayed by both parents for keeping this secret from her, distanced herself from the Evans, spending more time in the magical world.
Lily even tried to find her birth mother. Figuring that perhaps she had been a witch, she spent hours looking through old records
But she could never find any trace of Amora Incantare.
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For those of you that don't make the connection, Amora is the Enchantress, and Amora Incantare, is one of her aliases, according to the marvel wiki anyway. It's from Amora that Lily inherited magic, her beauty, and her green eyes.