Goddess of Yesterday is a reimagining of the Trojan War in Greek mythology. The story's protagonist and narrator, Anaxandra, lives on an unnamed island with her parents and brothers. To save their island from Nicander's attack, Anaxandra's parents let him take her as a hostage. Despite her sadness over leaving home, she becomes close friends with Princess Callisto, the disabled daughter of King Nicander.
The pirates' invasion of the island ruins Anaxandra's quiet life once again. Everyone gets killed except her, and King Menelaus rescues her, thinking she's Princess Callisto. She hides her true identity from the king to save herself from slavery. Although Anaxandra feels bad for impersonating Princess Callisto, her survival depends on it. King Menelaus treats her well and gives her a place to stay.
Everyone welcomes Anaxandra to the palace except Helen, who's suspicious of Princess Callisto's identity due to her red hair. The dislike Helen feels for Anaxandra turns into hatred for her, and Anaxandra lives in constant fear of being caught by Helen. Menelaus travels to Crete to pay tribute to the king. At the same time, Prince Paris of Troy attacks Sparta and steals everything, including Helen. Helen's daughter refuses to leave Sparta. As Hermione's replacement, Anaxandra protects Pleisthenes, Helen's infant son.
In Troy, Helen feels overwhelmed by the appreciation from the citizens of Troy that she forgets about her infant son. During her stay in Troy, Paris' sister, Cassandra, and Andromache become friends with Anaxandra, and away from Helen, she spends her time with them. Cassandra's prediction of the fall of Troy because of Helen fills Anaxandra with worry. She loves Euneus, king of Lemnos, and wants to be with him, but Anaxandra feels she must repay Menelaus for his kindness by returning his son to him safely before the war destroys everything.
