They were made to forget. But they'll never forgive.
Everything about Anna's life is a secret. Her father works for the Branch, at the helm of its latest project: monitoring and administering treatments to the four genetically altered boys in the lab below their farmhouse. There's Nick, solemn and brooding; Cas, light-hearted and playful; Trev, smart and caring; and Sam... who's stolen Anna's heart.
When the Branch decides it's time to take the boys, Sam stages an escape. Anna's father pushes her to go with them, making Sam promise to keep her away from the Branch, at all costs. There’s just one problem. Sam and the boys don’t remember anything before living in the lab—not even their true identities.
Now on the run, Anna soon discovers that she and Sam are connected in more ways than either of them expected. And if they're both going to survive, they must piece together the clues of their past before the Branch catches up to them and steals it all away.
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Anna feels strangely drawn to the boys in the lab in the basement of her house, so she started sneeking down there at night, when her father was sleeping, quite some time ago. Now she no longer has to sneek, because she's helping Arthur with his work and thus is permitted into the lab. She likes spending time there, helping her workaholic of a father, and seeing the boys, of course. Now Sam has asked her to sneek around some more: in the boy's files she's not permitted to see. Because she loves him, she does, but she does not get the chance to tell him anything because Arthur's superiors from The Branch come to get the boys, and they have to prepone their planned escape. In the process, they kill the agents who came for them, and Anna sees them, especially Sam, from a side she doesn't know, even fears. Sam shoots Arthur so he wouldn't be suspected of helping the boys escape, shocking Anna even more. Yet he urges her to flee with them instead of staying behind with him, making Sam promise he'll protect the girl from The Branch at all costs. He even gives Sam a clue where to go in order to regain his lost identiy.
There are several questions that come up right in the beginning, but one is the most pressing, something Sam mentions to Anna: If you try to build the perfect soldier, you don't lock him away. You put him in the field for testing. Good point, so why where the boys locked in there for a whole of five years? It's true they are dangerous, and might seem unable to control, considering they just broke out, yet it still doesn't make too much sense. However, there's a logical answer at the end of all of this!
Being tuned into each other by their alterations, the boys have no choice but to stick together. However, Nick wants to get rid of Anna because she reminds him of the lab too much, of being locked in like an animal for five years. Yet, since Sam's the leader of the group, she stays. They follow the clues Sam left behind for himself, trying to remember what was wiped from his mind.
Finding money in Sam's safe house, the group leaves for the city. There The Branch finds them, and to their surprise they try to get to Anna first. In the aftermath of it all, the boys realize that they want to protect her at all costs, even Nick. It's an urge that can only be another alteration. Maybe there's more to Arthur pressing her to leave with the boys?
Then they meet Sura, Arthur's divorced wife, and the woman that Anna knew to be her deceased mother. The first lie, and a shock to the girl. But Sura wants to help the group with intel, since she used to work for The Branch as well. She knows that Sam has stolen something from them and hid it, that's what the clues are for. It's also one reason his memory was wiped. She also tells Sam that the girl in the picture he found was his former love, Dani. Another shock for Anna. However, when Anna is unable to sleep at night and finds Sam to talk to, he promises her not to leave, and they share a kiss.
When the safe house is discovered, Cas is captured and Sura is killed. Just before she was shot, she can jog Anna's memory -- that she has nothing vivid of her childhood, because her memories have been altered. That's yet more to digest for the girl. But there's still more to come. For one, finding out that Dani and her younger sister disappeared years ago from their home, their parents' murders still unsolved. Curious enough, but most importantly: Dani's younger sister was called Anna. That's right, the Anna we know is the younger O'Brien sister, captured and altered by The Branch to control the boys as their commander. That explains the two incidents they obeyed her and why they feel the strong urge to protect her. It also explains Anna's urge to be close to them, and why they were holed up in the lab for years: they were testing how the alterations bonded them, the interdependency.
As they follow the clues to the latter, they dig up files that would cost The Branch the immunity from the government because they tired to sell off the boys to other countries. However, just as they try deciding what to do with that information, they are caught again. Trev, the one of the boys Anna viewed as her best friend and trusted the most, was originally part of another group and this transfered to their group as an undercover agent for The Branch. Sam is captured and Nick is wounded protecting Anna, yet she manages to grab the files on her escape.
Now Arthur is the only one Anna has left to help her, and he comes to their aid. Nick gets patched up, then they march right into The Branch to get the others back, ensuring the files to be published if they don't return until a certain time. However, all of them are thrown into cells without being listened to. But Anna is, of course, not a harmless girl at all so she manages to break out and get to the boys in the lab inside The Branch, and gets them out of their glass cells before Riley and Connor catch up with her.
In the following fight, Sam and Arthur are both shot, and Anna kills Riley. On their way out, Trev helps them. Although he believes Anna that The Branch is just using him, would betray him even, he stays behind. Of course he lost the groups' trust, although he confesses that he enjoyed being in Anna's company and tried to be as true to her as possible. They still leave him with the promise that if he ever tried to pull something on them again, they'd kill him.
In the end, Anna and Sam visit the grave of her parents before they move on. She's with the boys, but Connor got away, so they're still targets. The alteration of her being their commander is bound to wear off, but it's not sure when. It's still undetermined what's going to happen next.