A teenager is pulled from the wreckage of plane crash, and no records exist about her. Her discovery makes headlines. The mystery around her thickens when she wakes up in the hospital with amnesia. She has no recollection of her past. Though she can remember how to talk, she appears to have lost the knowledge of things like televisions and cars. She is soon called Violet because of her extraordinary violet eyes.
The girl confounds the doctors because she has no injuries from the plane crash. The only clue to her past is a locket with a symbol of two interlocking hearts and the inscription Z+S=1609. One night, after having been given a sedative, Violet sees a young man at her bedside. He holds her hand and asks if she remembers him.
Although her conscious self can’t, her unconscious tells her she does. He tells her not to worry, that he is going to get her out of the hospital. He removes her various tubes and wires. He then takes her hand and disappears in front of her. She wonders whether she dreamed the boy, but recognizes him in the crowd outside the hospital when she is released to the custody of a foster family, the Carlsons.
Heather and Scott Carlson bring her to their home on the central coast of California. Their 13-year-old son, Cody, also lives with them. When Violet changes her clothes before bed, she discovers a piece of paper with the words trust him written on it. Frustrated at the cryptic nature of the paper and her locket, she vows to put them away and forget them. She will start a new life and make new memories.
The next day she goes to the supermarket with Heather. While Heather returns to the store for a forgotten item, Violet loads the bags into the car. The boy from the hospital approaches, asking again if she remembers him. He explains her name is Seraphina, Sera for short. He says that she was never in a plane crash. She doesn’t believe him until he mentions the locket. He tells her that he gave it to her. Before Heather returns, he warns Sera, the name she realizes is her name, not to trust anyone. Dangerous people are looking for her.
Sera tells others that she’s remembered her name. She now believes that if she can return to the airport where she boarded the plane, the location may spark a memory. She knows her foster parents would not approve, so she asks Cody for help. He refuses because he and his friends are struggling to complete an extra-credit proof for their math class. It is one that mathematicians have been struggling to solve for over 100 years.
Sera makes a deal with him: If she solves his proof, he needs to help her get to the airport. She solves it in a few minutes but can’t explain how. The following morning, she and Cody sneak out to the bus station. While he buys the tickets, Sera speaks with an old woman. When Cody returns, he asks how she knows Portuguese, as that is the language she was speaking. Sera has no idea.
Seeing the airport does not help Sera’s memories return. No one at the airport will give her information either. Frustrated, Cody and Sera leave. An airline worker stops her outside the airport. Even though she could get in trouble, the woman tells Sera that she was checking the boarding passes for the passengers on the fated plane. She has no recollection of Sera boarding the plane. The teenagers return home, and Cody is grounded for his role in their excursion.
The following day, Heather takes Sera to the mall to buy new clothes. The same strange boy finds her there. He tells her his name is Lyzender, Zen for short. He alludes to the fact that they have been intimate before and that what she thinks is a tattoo on her wrist is actually a tracking device. A company called Diotech kept her in a lab before they escaped. As she storms away, he quotes a poem. Her subconscious mind immediately responds with the correct verses. Frightened, Sera runs to Heather and they go home.
Although he is furious at her for getting him in trouble, Cody helps Sera look the poem up on the internet. The words turn out to be from a Shakespeare sonnet written in 1609. Sera realizes that the inscription on her locket stands for Zen, Sera and the date. Heather, Cody and Sera meet Scott for dinner in town but Sera cannot stop thinking about Zen’s claims.
Already on edge, Sera panics on the way home when she sees a man walking along the road. She recognizes him from the bus ride to Los Angeles. She realizes he has been following her and that he now knows where she lives. As Heather parks in the garage, Sera kicks at the car door and it tears off. Sera overhears Heather and Scott arguing about her. She decides she must leave the Carlsons’ home.
She sneaks out that night and finds her way to a diner. The same man is there. He does not attack her; in fact, he pays for her dinner and tries to protect her from a publicity seeker. When Sera leaves the diner, reporters accost her. Then she sees a large man dressed in black. Her wrist tingles as a device he is holding lets out a beep. The man smiles and starts toward her. Sera flees into the woods. Eventually the man in the diner catches her. He uses a device called a modifier to render her unconscious.
When Sera wakes, she is chained to a chair. The man who captured her is named Rio. He was instrumental in creating her and programming her mind. She is not a robot, but neither is she completely human. Zen finds them and holds a gun to Rio. Rio tries to convince Zen that he is on their side, that he wants to help Sera escape, but Zen does not believe him. He and Sera run away, and he takes her to the empty school where he has been living.
At the school, Zen produces a cube that contains many of Sera’s memories. One by one, he lets her see how they met — when Zen scaled the wall to the compound where she was kept. Even though Rio and other scientists erased her memory of him daily, Zen would find his way back and continue their relationship. She comes to realize how scientists have manipulated her life and finds comfort in Zen’s presence.
In the morning, Cody finds them at the school. Zen holds him at gunpoint. He is sure the man is working for Diotech. Cody convinces Zen otherwise. Cody helps them get a car, and then heads home. Zen has Sera flip through the owner’s manual, and she discovers she has gleaned enough to drive.
When they stop to get gas, she is recognized again. A woman takes her picture and puts it on social media. Immediately, Sera’s tattoo vibrates and two more men in black show up at the gas station. Zen orders her to run. She turns to see the men take him prisoner.
Sera flees to another diner and calls Cody for help again. The two search the internet for Diotech. Although no company exists with that name, the search continually pulls up a blogger named Maxxer. Just after Sera arranges to meet Maxxer, her phone rings. The call is from Alixter, the head of Diotech. He has Zen and will kill him unless Sera turns herself in.
Maxxer pulls up outside of the diner. She is a former employee of Diotech. She tells Sera that Diotech exists in the future. The scientists found a way to manipulate genes so people could travel, or transgress, through time. Zen and Sera had planned on transgressing to the year 1609 so they could be together and not be found, but something went wrong. Sera did not go to 1609, but rather landed in the ocean amid plane wreckage.
Maxxer takes Sera to the remote area where Alixter is holding Zen, but does not follow her to the cave. Alixter pontificates about how they should have made an adult version of their experiment because teenage girls are far too unpredictable. They had hoped a younger creation would be more pliable.
Rio arrives to try and help Sera. Before Alixter uses a modifier to burn his memories, Rio tells Sera that he hopes she can find it in her heart to forgive him. Sera realizes he has sent her a code, but cannot decipher it.
Alixter is unable to transgress with Sera back to their time in the future. Zen explains that something has happened to her genes, which causes her to be unable to journey through time. A memory floods Sera’s mind, and she remembers Rio giving her the ability to turn the gene off by using her locket.
Sera tells Alixter that she knows how to fix the gene, but he must first let her say goodbye to Zen. When she kisses Zen, with her locket open, she is able to transport them both out of the cave. Alixter and his thugs come after them. Zen asks Sera to trust him. They join hands and leap over the side of a cliff.