Earth has fallen to the Souls, an alien race that inhabits “host” life forms and erases the host’s ability to control their own body. Only small pockets of free people remain, and they would rather die than allow a soul to inhabit them.
The Seeker (Diane Kruger) chases Melanie (Saoirse Ronan), a free person, through an abandoned hotel. Melanie jumps through a window and falls many stories hoping that she will die and that her body will be useless to the Souls. Powerful alien medicine saves her life, though, and the Seeker implants a Soul in her. The Soul, who has visited many planets and has inhabited many life forms, asks to be called Wanderer (Saoirse Ronan). The Seeker wants to use Wanderer to discover information about any remaining free people. On her first night in Melanie’s body, Wanderer discovers that Melanie’s soul and mind survived her implantation. Melanie promises to fight Wanderer for control of her body.
Soon, Wanderer begins to tell the Seeker all about Melanie. She and family initially avoided the invasion. When Seekers finally found them, Melanie’s father killed himself, leaving Melanie to care for her little brother Jamie (Chandler Canterbury). Melanie, whose voice only Wanderer can hear, screams at her for telling her about Jamie. Wanderer also learns about Jared (Max Irons), who Melanie met when she was scavenging a house for food. Jared, also a free person, joins Melanie and Jamie. For a time, the three of them live in the desert, and Melanie and Jared eventually become lovers. Melanie hates Wanderer for telling the Seeker about her past, and for the first time, Wanderer begins to question whether or not her people are actually good. They do not lie, and they do not hurt others, but at the same time, they steal other life forms’ free will.
The Seeker suspects that some of Melanie’s spirit might linger within Wanderer, and she warns the latter against the powerful emotions humans have. Wanderer also tells the Seeker that Melanie, Jamie, and Jared left their desert home when they spotted Seekers nearby, but she does not know where they went. The frustrated Seeker leaves Wanderer, who then sees several of Melanie’s memories: her Uncle Jeb (William Hurt), a house in the desert, and a rock formation. Wanderer sketches the rock formation, but a distraught Melanie begs her to destroy the drawing; it could lead the Seeker to Jeb’s home, where the trio was headed at the time of Melanie’s capture. Wanderer tears the drawing apart and stops giving new information to the Seeker.
Eventually, the Seeker decides to implant herself in Melanie’s body and find a more placated host for Wanderer. Melanie begs Wanderer to escape; she will take Wanderer to her Healer, the person who implanted Wanderer in Melanie’s body, because they do not think he would follow the Seeker’s plans. Melanie fights Wanderer for control of her body and gets her as far as the balcony of her apartment. Melanie manages to propel her body off of the balcony, and Melanie/Wanderer land in deep pool under the window. Melanie wants to steal a car, but Wanderer stops an old man and, simply by telling him she needs his help with something important, convinces him to give her his car. The Seeker discovers Wanderer’s escape and also finds the torn up drawing in Wanderer’s pants pocket.
Melanie tricks Wanderer into taking her to her uncle’s hideout, and when Wanderer tries to turn the car in the opposite director, the pair fights for control of the body. The car swerves off of the road, rolls over, and is totaled. Melanie instructs Wanderer to walk into the desert and reminds her to step on rocks so she will leave no tracks. Wanderer/Melanie stumbles through the desert for hours before Wanderer passes out under a tree. Luckily, her Uncle Jeb finds them, though he is horrified when he sees that Melanie now has bright blue irises, the mark of an inhabited person. Everyone in his search party, including his wife Maggie, wants to kill Wanderer/Melanie. Instead, Jeb blindfolds her and takes her back to their hideout.
Meanwhile, the Seeker has been searching for the rock formation Wanderer sketched in a database. She finds the formation and drives into the desert to find it. When she sees the wreckage of Wanderer’s car, she calls for reinforcements. More Seekers arrive, but they doubt Wanderer could survive for long in the desert. While the Seeker chooses to stay put, her colleagues soon return to the city.
When Jeb removes the blindfold from Wanderer’s eyes, she finds she is in a cave. Jeb found a series of interconnected caves within a large rock formation, and since then, many other free humans have joined him. Wanderer meets Doc (Scott Lawrence) as well as brothers Ian (Jake Abel) and Kyle O’Shea (Boyd Holbrook). Jared sees her too, and when Melanie makes her body run towards him, he hits her hard enough to knock her out. Jared and Jeb take Wanderer to a holding cell. When she regains consciousness, Melanie warns her not to tell anyone that Melanie still exists, because they will think she is lying. Eric, Ian, and Brandt (Mustafa Harris) arrive with the intent to kill Wanderer, and Jared fights them. Wanderer bursts from her cell and begs them to take her, not to hurt Jared, and Jeb arrives in the nick of time. He takes the next watch over Wanderer/Melanie, and he shows her kindness.
Jeb shows Wanderer all of the features of the underground caves: water pools, an underground river with a quick current, solar powered lamps, and a huge underground wheat field. He also gives her the nickname “Wanda.” Jeb and his companions installed hundreds of mirrors at the top of the cavern to reflect sunlight down into the cave, which is how they grow some of their food. He wonders if, when Souls inhabit humans, the humans always die. He knows he would fight a Soul “like hell” to maintain control of his body, and no one had fight like Melanie. He also tells Jamie to come out of hiding, and when the boy emerges, he tells Jamie to watch over Wanda.
Jamie takes Wanda to a part of the caves that is lit by thousands of glowworms. He tells Wanda he misses his sister so much, and we discover that, on the night Melanie jumped from the hotel, she and Jamie and Jared were hiding in the hotel. Melanie left Jamie in hiding and promised to come back for him before running away to distract the Seekers. Melanie gives Wanda permission to tell Jamie that she’s still alive. Jamie embraces her, and the two fall asleep together in Jamie’s room.
The Seeker receives word that humans have been spotted in the area, and reinforcements will come after all.
Jeb wakes Jamie and Wanda. He wants them to help harvest the wheat. While they’re harvesting the wheat, they hear the sound of helicopters, and Jamie accidentally cuts his leg with a scythe. Wanda helps the others turn the giant wheels that retract the mirrors, but the Seeker, in a helicopter, sees a glint of sunlight reflecting off one of them. Her colleague thinks she mistook one of their shiny cars for evidence of humans, and once again, the search is called off.
Eric, Jared, Brandt, and Aaron (Lee Hardee) leave the caves in large trucks. They go to a giant grocery store and gather tons of food. When a Soul catches them, they knock him out. They drive back to the caves, but the truck carrying Brandt and Aaron is going too fast, and some Seekers in a helicopter try to stop them. Brandt and Aaron open fire on the helicopter and try to drive away. Dozens of Seekers arrive on the scene and corner them; Brandt drives the truck into a cement partition so neither will be taken alive. The Seeker notices the truck driven by Eric and Jared take off, and she pursues them. Eventually, they slam on their breaks so she will drive her car into their truck. When Eric and Jared jump out of their truck, one of them drops a gun. The Seeker grabs the gun but accidentally shoots her partner in the head. More Seekers arrive on the scene and chastise her for her aggressive behavior and for murdering another Soul. They believe the human resistors will die off on their own, and they think the more dangerous war is the one waging within her. The Seeker storms away, muttering that they are not in control.
In his brother’s absence, Ian has grown fond of Wanda, and she of him. He believes, like Jeb, that Melanie must still exist inside of Wanda, because she tried to risk her life to save Jared from being hurt. He eats meals with Wanda, Jeb, and Doc, and Wanda tells them about her travels. Their camaraderie is broken when Eric and Jared return with news of Brandt’s and Aaron’s deaths. Ian takes Wanda back to his room so he can protect her, because now the free people dislike her even more. Jared pays Wanda a visit, and he angrily tells her how much he misses Melanie. He wishes he could kiss her one more time. Melanie wants to both kiss Jared and to keep Wanda from kissing him, but eventually, the first impulse overcomes her. Wanda/Melanie kisses Jared for a few moments before Melanie slaps him away, angry that she let Wanda kiss her boyfriend too. Jared realizes that, because Melanie slapped him for kissing her the first time, she must still be alive inside of Wanda. Now, Melanie has another defender.
Life continues. More and more people begin to suspect that Wanda and Melanie are both living inside of one body. Ian takes Wanda outside, on the top of the rock formation, because she misses the outdoors. Melanie doesn’t want Wanda to get close to Ian, because it makes her feel disloyal to Jared, but Wanda and Ian are slowly falling in love. Wanda tells Ian he only cares for her body, that he would crush her if he held her actual body in his hands, and he denies that charge. Ian asks if Melanie would let Wanda kiss him, and even though Melanie protests, Wanda kisses him anyway.
Back at Seeker headquarters, the Seeker stares at the rock formation angrily. Someone tells her she will never win, and the Seeker grasps her head.
Wanda sits by the river, and Eric finds her. Melanie tells Wanda to run, but Eric eventually catches her, and he tries to throw her into the river. Wanda pivots, and instead, Eric flies into the river. Wanda grabs his hand to keep him from being swept away, and when Ian and Jared find them, they quickly deduce that Eric tried to kill Wanda. Jeb, Jared, and Ian want to exile Eric, but Wanda will not say that Eric tried to kill her, so they let him go. Jared and Eric leave on another mission, and they return with several unconscious bodies, which Doc hustles into his lab. Jamie’s leg has gotten worse, but when Wanda finds him, he tells her that Doc is busy. Confused, Wanda goes to his lab, even though Melanie screams at her not to stop. Wanda discovers several corpses and many crushed Souls Doc has been extracting them from implanted people and has killed the Souls. Jared, Ian, and Jeb catch her, and she calls them murderers. She screams at Melanie to get out of her head, and she runs away and cries.
After several days, Melanie has not returned to her head. Wanda kisses Ian in the hopes that Melanie will become angry and return, but that doesn’t work. Next she kisses Jared, and Melanie comes roaring back into her head. Jamie has gotten much worse, and Wanda says Soul medicine will save him. She has Jared drive her to a Soul medical facility. She cuts herself and is healed within seconds by a Healer. She manages to steal medicine, and she and Jared return just in time to save Jamie.
Wanda takes Ian and Jared to a grocery store, where her glowing blue irises allow her to take as much food as she wants without causing a hassle. On their way back to the caves, however, the Seeker catches them. A scuffle ensues, and once again, Jeb arrives just in time. He shoots the Seeker in the shoulder, and they take her as a prisoner.
Wanda tells Doc she will forgive him if he extracts the Seeker’s Soul from her body. While at the medical facility, Wanda also stole one of the pods used to store Souls. She will send the Seeker to another planet, and because it will take decades for the Seeker to arrive there, everyone will be safe. Wanda also wants Doc to extract her from Melanie’s body to let her die, because she no longer wants to steal the free will of another being. Melanie protests, because now she loves Wanda. Wanda shows Doc how to extract a Soul from the Seeker: by coaxing it out and treating it with love. The woman the Seeker possessed wakes up and is overjoyed to have control of herself again. She says the Seeker pursued Wanda because she knew, personally, that humans could fight back against Souls.
Wanda says goodbye to Ian before going into Doc’s lab. She lies down on the table, and she and Melanie share one last conversation. Melanie calls her sister. Wanda closes her eyes, and when she reopens them, she sees Doc, Ian, Melanie, Jamie, Jared, and Jeb standing over her. Wanda has been unconscious for a month, and in that time Doc has extracted dozens of Souls from humans. Wanda’s new body did not wake up on its own and started to die, so they placed Wanda inside of her. Wanda forgives Doc for breaking his promise, and she and Ian kiss.
Months later, Wanda, Ian, Melanie, and Jared are driving through a city when a Soul pulls them over. He inspects each of them and is surprised to see that Wanda, a Soul, is working with humans. He then reveals that his associates are also free humans, and that he thought he was the only Soul who “changed sides.” There are several other bands of free humans, which gives everyone hope.
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