In the 1840s, the dedicated fossil collector and paleontologist Mary Anning supports her ailing mother, Molly Anning, while managing a small shop in Lyme Regis, Dorset. Every day, Mary explores the beach during low tide, on the hunt for fossils, with tiny ammonites being a frequent discovery. Upon returning home, she helps her mother wash and polish a set of eight delicate animal figurines.
One fateful day, a geologist named Roderick Murchison arrives at Mary's shop with his wife Charlotte in tow. He is captivated by Mary's impressive work and proposes to pay her for a guided trip where he wishes to learn the art of fossil hunting from her. Though initially hesitant and a little antagonistic, Mary ultimately agrees to his proposal. However, during dinner at the Three Cups, Roderick's cold demeanor quickly surfaces as he informs Charlotte that now is not the right time for them to have another child.
Following their visit to the shoreline, Roderick discovers that Charlotte has fallen into a depressed state, confined to her bed. Returning to Mary's shop, he reveals that Charlotte has been sent to Lyme Regis for recuperation and seeks Mary's help as he prepares for a six-week expedition to Europe. Mary, seeing an opportunity for financial gain, reluctantly consents. As time passes, Charlotte begins to join Mary on her morning fossil hunts.
After an ocean bath meant to aid her recovery, Charlotte falls ill and develops a high fever. Under the care of Dr. Lieberson, who prescribes bed rest, Mary takes on the role of her nurse. In an attempt to help Charlotte heal, Mary visits her friend Elizabeth Philpot for some healing salve, though she declines Elizabeth's invitation to come indoors. As Charlotte regains her health, she becomes increasingly involved in domestic chores alongside Mary, even crafting a mirror frame together from cowries. In a poignant moment, Charlotte learns that the figurines Molly cleans every day symbolize her eight deceased children, deepening her emotional connection to Mary.
When Dr. Lieberson invites Mary to an evening recital, she agrees but insists Charlotte joins her, believing Charlotte is fully recovered. At the event, Charlotte mingles with the townsfolk, while Mary feels a twinge of jealousy, smoking outside in the rain and watching through the window. After enjoying a spectacular magic lantern show, Mary returns home in the downpour, where she finds Charlotte who discovers her writing a poem in her journal.
Using driftwood from a beached boat, Mary and Charlotte successfully transport a large rock to the shop, uncovering an ichthyosaur fossil inside, reminiscent of one Mary had discovered as a child and sent to The British Museum. As they prepare for bed, their bond deepens, culminating in a kiss followed by an intimate encounter. Their relationship flourishes with joy-filled swims in the ocean and shared meals.
However, the tranquility is shattered when a letter arrives from Roderick, demanding Charlotte's return to London. Devastated, the two women share a passionate night before Charlotte's departure. Following a tragic incident, where Molly suffers a fall and passes away, Mary is left in despair. Elizabeth visits Mary to offer her condolences and reminds her not to forsake her relationship with Charlotte, akin to how she had abandoned their own bond after her father's death.
Eventually, Mary receives a letter from Charlotte urging her to travel to London. Upon arrival at the Murchison home, Mary is struck by the sight of one of her large ammonite fossils prominently displayed in a glass cabinet. Charlotte takes Mary upstairs to reveal a beautifully furnished bedroom intended for her to move into. Flustered, Mary confronts Charlotte about this surprise revelation, feeling as though her life is being disregarded. In her frustration, she leaves, accusing Charlotte of trying to confine her in a "gilded cage."
Finally, in the museum, Mary roams through the vast halls filled with art. She is overcome with emotion as she approaches the exhibit displaying her original ichthyosaurus, only to find that there is no acknowledgment of her contribution. At that moment, Charlotte arrives, and the two women share a poignant gaze from opposite sides of the glass, amidst the oblivious museum-goers admiring the exhibits around them.
