Continuing from the previous novel, The Darkest Minds, Ruby is living her life in the Children's League now. She is on a mission with her team to retrieve an important prisoner from the PSF's. That prisoner is none other than Liam's older brother Cole.
Next, there is a back flash to Ruby's experience's when she first arrived to the Children's League and how she met the rest of her team: Vida, Jude and Nico and how she was trained to interrogate the prisoners the leader Alban ordered her to.
Back to the present, Alban calls for Cole and Ruby in for questioning because her team leader Rob complained how she disobeyed his orders. That is resolved with Cole's persuasion because she is the one who freed him from the PSF's. Alban orders Ruby to get into Cole's mind to find some important information Cole seems to have forgotten about. That information is about a flash drive and Ruby sees Liam is connected to it so she lies to Alban about it.
Meanwhile, one of the kids was killed in a mission and Nico discovers security camera footage that shows League's agent Jarvis shooting the boy in the back. The kids are now aware that Rob, Jarvis and some of the other agent want them dead.
Ruby talks with Cole about the flash drive and Liam and tells her to go on a mission to retrieve it from him, because he accidentally brought it with him when he took Cole's jacket out of his apartment instead of his own. The flash drive contains important information about the IAAN and what caused it. Ruby agrees and is soon sent on a mission with Jude and Rob in charge. She suspects that Rob intentionally made Jude go with them in order to kill him.
In the middle of the mission Ruby escapes with Jude to go on Cole's undercover mission to retrieve the flash drive and informs Alban and rest of the agents about Rob killing two PSI kids with no reason.
On her way she comes across Chubs who is undercover as a skip tracer. Skip tracers are bounty hunters who capture PSI kids for money. Vida has been following them. All four set out to find Liam.
Ruby discovers that Vida is communicating with Cate and Vida explains to her that Cate is in on their plan and that she is on their side.
The group stumbles upon a pack of Blues with a vicious leader called Knox. Liam is in their camp too in a very bad condition. In a ring fight Ruby manages to take control over Knox without having to touch him and makes him leave the camp with messed up brain.
On a run for supplies Ruby gets badly injured and lost from the group. She is captured by Rob who works as a skip tracer now with a false name. Ruby takes control over Rob and he is killed in a car crash. Badly injured Ruby gets picked up by her friends.
Liam is better now but his mind is in confusion. Eventually, Ruby returns his memory back to him. Vida gets new information from Cate to meet in Colorado. Ruby and Vida are suspicious and realize that they were intercepted and that they aren't communicating with Cate but someone else.
They head off to Colorado and discover Clancy, president's Grey son, waiting for them. He tells them about the League's agents' plan in California to use the children as live bombs during president's public appearance to make a point and about Alban's death. They all head out with Ruby forcing him via Clancy's jet to California to stop them.
The group arrives to the Children's League building and Ruby realizes Clancy tricked her; kids are safe and waiting for Cate and Cole. Clancy wanted to get some documents from Alban's office about her mother but Ruby picks them up before he destroys them. The building is under attack by Jarvis and agents but Cole comes to the rescue.
Everyone seems to be safe and they are watching a TV broadcast about President's appearance. Suddenly, a kid appears in front of him and shoots him. There is an electricity blackout and the building is being bombed making the roof over them collapse. Cole starts to evacuate kids and agents out of the building.
Finally out, Ruby realizes Jude is missing. Liam and Chubs go in for him but they find him dead. Liam hands Jude's compass over to Ruby. A plane flies over dropping paper news about President Grey surviving the attempt and the bombing was his retaliation against the Children's League. Clancy appears and tells them that his father probably planned the attempt to have it a reason to attack. He also brags about destroying his mother's research about a cure to IAAN. Ruby shows him the papers he failed to destroy about the research.
