The film starts in a school cafeteria on what seems to be an ordinary day, until a little girl named Grace Somerfield (Grace DeAmicis) is sitting frozen, when her eyes glow and the can she is holding is crushed without her moving a muscle. Grace falls over and dies. We hear the voice of Ruby Daly (Amandla Stenberg) saying how Grace was the first of many children to die from a disease that would become known as IAAN (Idiopathic Adolescent Acute Neurodegeneration). We see President Gray (Bradley Whitford) discussing how his son has survived as a result of a cure they are testing out on infected children.
We then cut to a young Ruby (here played by Lidya Jewett) on her birthday as she celebrates with her parents Molly (Golden Brooks) and Paul (Sammi Rotibi). At night, Ruby goes into her parents' room and touches Molly's arm, at which point Ruby's infection appear to manifest. In the morning, Ruby goes into the kitchen, but Molly doesn't recognize her or know who she is. Despite Ruby's pleas, Molly locks her in a garage and waits for authorities to come and take Ruby away.
Ruby is brought to a camp, Thurmond, which is housing all the surviving infected children. One young man attempts to flee, only for armed guards to hold him down. He uses his mind control power to cause one of the guards to shoot themselves before the others detain the young man. Ruby is then brought to a testing facility where her powers (also of mind manipulation) classify her as an "Orange". The doctor testing her tries to inject something into her, but she touches his arm and has him classify her as Green.
Ruby spends the next six years at Thurmond with other Green kids. The others are separated into Blue or Yellow, but there are no Reds or Oranges because they were considered too dangerous. They are lorded over by the cruel Captain McManus (Wade Williams) and his band of mercenaries. The officers at Thurmond are testing a new subatomic frequency that causes the kids to recoil in agony and makes Ruby pass out.
Ruby wakes up in a bed spoken to by a Dr. Begbie, or Cate (Mandy Moore). She is significantly friendlier to Ruby that anyone else at Thurmond, and she wants to help Ruby. Cate leaves and slips Ruby a note saying that the others know she is Orange and that they are planning to kill her, so she tells Ruby to meet her in the boiler room. After doing so, Cate helps Ruby escape the facility just as the officers are looking for Ruby. As Cate attempts to drive away, she is stopped by a guard who almost notices Ruby, but Ruby uses her power to turn the guard away so that they can leave.
Cate drives Ruby to find a group called The Children's League so that they can protect her. She gives Ruby a tracking device to use in case they get separated. They meet at a gas station with Cate's boyfriend Rob (Mark O'Brien), who hands Ruby supplies. Ruby slips and Rob catches her, which lets her catch a glimpse into his memories, showing that he was among those who roughly handled the infected kids and presumably did bad things to them. She goes into the store and sees a little girl, Suzume/Zu (Miya Cech), who manipulates electrical currents and does so to try and get away from Ruby. She runs after Zu, trying to get away from Cate and Rob. Ruby pleads with Zu to let her inside, and she goes. The van that they are in then drives away.
The other two guys in the van, Liam (Harris Dickinson) and Charles/Chubs (Skylan Brooks), are nervous when they see Ruby in there, thinking she was sent to apprehend them, but she tells them she's a Green. As they continue to drive, they are pursued by a Tracer (bounty hunter) known as Lady Jane (Gwendolyn Christie). Cate and Rob also attempt to catch up. Ruby takes the wheel as Liam uses his power to pull trees and cause debris to send the cars offroad.
The kids stop driving, and Ruby attempts to leave so she can go home, but Liam stops her and says they are heading to the East River, which supposedly holds a compound where infected kids can stay, rest, and eat. After sharing a snack, they continue making their way toward East River, when Ruby mentions being taken to The League. Liam says they can't help her, as he was recruited by them to be a murderous soldier, so he abandoned them.
McManus finds out that Ruby has escaped, and he kills one of the doctors who studied her. He orders the Tracers to go after her.
Ruby looks into Zu's mind as she sleeps, and she sees a memory of when Liam used his powers to break a number of kids out of his camp, but some didn't make it because they were shot by officers. They then continue moving forward, stopping in a mall for supplies. They are then trapped by other superpowered kids who think they are Tracers. After explaining themselves, the other kids allow Ruby and her friends to stay for the night.
The kids all sit around a campfire talking about the East River compound. Ruby touches the skin of one of the mall kids and is told "EDO" and nothing else. Later on, after the others are sleeping, Ruby and Chubs hear a frequency on the radio calling out to other superpowered kids.
In the morning, Liam drives Ruby back to her old home, but when she gets there, she feels she can't go inside to her parents since she believes it's her fault that they forgot her after she erased their memories. She returns to the group, and they are ambushed by Lady Jane. Before she can take the kids in, Ruby grabs her hand and forces her to walk endlessly, even if she gets tired and hungry, and Jane complies. This works but also makes Ruby pass out, and the others realize she's an Orange.
Liam and Chubs argue over what to do with Ruby, but she overhears and just decides to leave so as to not cause them anymore trouble. They convince her to stay because while they are upset that she lied, they don't want her to go off on her own, and they tell her it's okay that she's Orange. The kids all continue walking down a trail until they find EDO.
At EDO, the kids meet Clancy Gray (Patrick Gibson), son of the president who was previously going around saying he's been cured, when in actuality, he just escaped the facility he was housed in and is providing refuge for other escaped children. He turns out to be an Orange as well, and he spends private time with Ruby so that he can help her harness her full potential, but Liam doesn't like how close they are getting. In secrecy, Clancy is messaging McManus.
Clancy tells Ruby how his father had him tested countless times until he just abandoned him. He takes Ruby around the compound so that she can test the strength of her abilities, like stepping into an argument between Chubs and another kid by manipulating the kid's mind. Chubs later tells Ruby how he feels the compound is no different than the camps they were at due to all the rules they have to follow.
Ruby goes to Clancy to ask if Chubs can use his computer to contact his parents, but Clancy refuses for thinking that Chubs may give away their present location. Instead, Clancy wants to figure out how Ruby can erase peoples' memories by stepping into her mind. He then tries to force himself onto her to try and erase that memory, but she pushes him off and goes back to her friends, trying to get them to leave the place.
That night, McManus and his goons show up to round up the kids for a harvest. Clancy emerges as the ringleader of the whole thing, with McManus telling him that his father is trapped in the same padded cell he was in. Clancy wants to use the kids as part of an army for revenge against his captors, with Ruby by his side since they are so powerful. Ruby makes McManus shoot himself in the head as Zu goes to hit the lights to zap the other Tracers with electricity. The kids run for it, but more Tracers descend upon the compound and unleash the Reds, who breathe fire at everyone. Liam uses his powers to shield his friends with a freight container, and then hurl it upon the Reds. Clancy goes for Ruby again, trying to tell her how he can fix her. She defies him and manipulates the pilot of a Tracer helicopter to come crashing down, letting Ruby and her friends get away. In the chaos, Chubs is hurt badly.
The next morning, Chubs is unconscious. The kids are found by Cate, Rob, and other officers, who bring them to The League. The kids are put in a hospital for recovery. Cate goes into Ruby's room to convince her to stay with them and help change things since she is so strong and rare among the other kids. When Rob steps in, Ruby manipulates his thoughts so he can leave her alone. Ruby wants them to let Liam go so that he won't have to kill for them. She goes into Liam's room and spends one last moment with him before she kisses him and erases all his memories of her. Thus, he is free to go and follow his own path.
In Ruby's closing narration, Liam runs off on his own, while we see that Clancy survived and is being taken into custody. Cate brings Ruby to a stadium full of kids as she prepares to lead them toward a new future.
*CUT TO THE CHASE*
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A disease known as IAAN wipes out over 98% of the children in the United States. Those that survived developed powers that the government found dangerous, so they were all put in camps to test them and eliminate the most dangerous ones.
Ruby Daly is an "Orange", as she has the power to manipulate people's thoughts and actions. She accidentally erased her parents' memories of her as a child, and she spends six years at a camp, Thurmond, until she is broken out by a sympathetic doctor named Cate. She wants to take Ruby to a group called The Children's League so that they can protect her, but Ruby ditches Cate when she sees that her boyfriend Rob was among the mercenaries that manhandled the children.
Ruby teams up with three escaped children - Liam, Chubs, and Zu - as they head to find a compound that holds refuge for other superpowered children. They find the place and meet the leader, Clancy Grey, son of the president who was supposedly cured, but instead turned against his father after he abandoned him. Clancy, who is also an Orange, takes an interest in Ruby to see how they can use their powers together. Clancy turns out to be a creep who is working with those at Thurmond to round up the other superpowered kids as part of his own little army to turn against those that hurt him. After the Thurmond mercenaries show up, Ruby and Liam team up to take them all down before escaping.
Cate finds Ruby and her friends and brings them to The League to recover. Ruby agrees to join Cate on the condition that they let Liam go, as he was originally a soldier for The League, but he did not want to kill for them. Ruby reluctantly erases Liam's memories of her so that he won't feel compelled to stay there.
Ruby steps forward as a leader for all the other kids so that they can live toward a better future.
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