The book is "two-sided" but follows the same plot through both Lyra and Gemma's eyes so I will be summarizing both as one rather than doing separate viewpoints.
When the book begins we learn that Lyra is a "replica", which is another word for a clone. She lives at Haven, a research facility on an island which I think is in Florida if I remember correctly. It is a top secret facility which harbors many replicas that are made at Haven, cloned from real children stolen or bought from their parents (more on that later).
Lyra is mostly content with her life at Haven, and abides by the rules other than hiding the fact that one of the nurses there taught her to read. The mainlanders have always had stories about the things that go on at Haven though, and one day one of them breaks in to the compound with a bomb strapped to themselves and blows it up. Lyra is outside when this happens and she and another replica, a boy called 72, barely escape in the ensuing chaos.
In the marshes surrounding the compound they meet up with Gemma (who we think is human but actually turns out to be a replica) and Jake (whose dad was killed by the government for finding out the truth on Haven) and they help them finish their escape. Gemma has run away from home to go to Haven to find out what all the mystery is with it since her dad was involved with the funding of it under the guise that she is going to Florida to see her friend Alice. She hitches a ride there with a boy from school named Pete.
Once back on the mainland they all begin researching everything about Haven, and they find out that the replicas are being made just to have different diseases and vaccines tested on them. Lyra thought all the tests and shots given to her throughout her life were because clones are frail and get sick easily but it was really because they were being injected with different diseases and slowly being killed to see the effects.
Gemma learns that Lyra isn't actually a clone when she and Jake are held hostage by a man that wants to know what they know about Haven because his daughter was taken from him when she was young. He thinks they know something since Gemma's father used to be one of the main supporters of Haven (until he found out exactly what they were doing). Gemma realizes when the man mentions a scar over his daughter's eyebrow that Lyra is actually his daughter.
Lyra and 72 ran away from Gemma and Jake before all this happened because Jake is afraid they are being chased by the government and staff from Haven and he's distrustful of Gemma and Jake. Lyra trusts 72 so she goes with him. They end up falling in love (of course).
Lyra and 72 try to find the nurse who taught Lyra to read since Lyra thinks she's the only one who can really help them but they find out that the nurse had been killed since she planned on leaving the research facility and revealing what she knew to the public via Jake's dad.
In the meantime, Gemma and her (now boyfriend) Pete find out that Gemma is actually a clone herself, and that her mother and father had taken her from Haven when she was a baby since she was a clone of their own daughter who died.
Lyra and 72 call Gemma from Jake's phone when they find that Jake has been killed at his home since they know they are in grave danger and they all join back up now that they know the truth and proceed to go back to Gemma's home to decide what to do next.
On a side note, this summary isn't as detailed as most I do because it hasn't been announced that this will be a series. From the ending it had I feel it will be, and if so I may go back in and add more detail, but this at least gives the gist of the events in the book for now. Thanks for reading! :)