This post contains lots of spoilers!!
This book is told in alternating viewpoints between Alina, Bea, and Quinn. They all live in the pod, which is basically a big domed city that provides oxygen because there is almost none in Earth's atmosphere. The reasoning behind why there isn't any oxygen left is a little shaky, but I'll go with it. Life within in the pods is very class structured. The Premiums are at the top and then there's auxiliaries that live in Zone 2 and Zone 3 (3 is the worst).
Quinn is a Premium. He tries not to take his charmed life for granted. He does dumb things, but in kind of a sweet, endearing way. Bea is his best friend who has a crush on him. She lives in Zone 2 but is trying to get into a special government program that would lead to her becoming a Premium. Alina lives in Zone 3 with her aunt and uncle and cousin Silas because her parents are dead. She is part of the Resistance.
Alina needs to escape the pod because of a mission gone wrong. Abel, the boy she was on a mission with, has turned up dead. We learn later than Abel was not actually part of the Resistance, but we don't find out more, namely if he was the one who sent the government after Alina. Quinn and Bea are leaving the pod on a planned camping trip. (If air is so precious, it seems dumb to waste is on a multi-day camping trip, but whatever) Quinn has an instant crush on Alina, so he decides to help her leave the pod.
They are all able to leave and decide to stick together for a bit. After a while, Alina leaves them, but Quinn decides to follow. Bea is pissed but follows as well, which is good because Alina has come across trouble. She's run into a drifter named Maude. A scuffle ensues and they disarm Maude. Bea befriends Maude somehow and even though Alina wants to kill Maude, Bea convinces them to bring her along.
Alina tells them about the Resistance. They are growing trees, even though the government keeps trying to destroy them. The government wants everyone to remain captive in the pods. They even pump more oxygen than necessary (30%) into the pod to keep them used to a higher amount. The Earth currently has been restored to 6%, which some of the members of the Resistance have trained themselves to be able to stand. Bea is shocked and wants to join up. Quinn still just wants in Alina's pants. So they want to follow Alina to the Grove.
A tank shows up and Quinn is buried in the rumble of a building, while Alina, Bea, and Maude are able to escape. Bea wants to go back for him but Alina insists they don't have the extra oxygen and that they'll return for him once they refuel at the Grove. Quinn survives the attack and while he's unable to move, he realizes his feelings for Bea. Of course he's loved her all along! Alina's cousin Silas and friend Inger come along looking for her, and instead finds Quinn. He decides he can tag along.
Bea, Alina, and Maude steal a government tank and make it to the Grove with just enough oxygen to spare. The Resistance leader, Petra throws Maude and Bea into a cell. Soldiers come upon Quinn, Silas and Inger. Quinn is shocked to discover that his father is the general in charge and is horrified when he murders Inger. Silas and Quinn finally make it to the Grove, where Quinn and Bea reunite and kiss.
The government is coming to destroy the Grove, where they've managed to grow a decent amount of trees and plants. Petra decides that the best plan is to get Quinn and Bea to lead them off-track. So Quinn and Bea get "rescued" by a tank and pretend to have been kidnapped and escaped from the Resistance. They tell them that they were to the south, instead of their actual location. This gives the Grove a few extra weeks, which they use to recruit extra drifters, with Maude's help, and train them to fight. It isn't enough however, and the soldiers destroy the Grove and kill most of the Resistance. Alina, Silas, Dorian (another Resistance member who can breathe outside), Maude, and Bruce (another drifter) are able to escape.
Eventually the Pod Minister (the leader of the pod) discovers that Quinn has been lying and forces him to do a press conference. If he doesn't, then he threatens to hurt his family. But Quinn instead tells the truth at the press conference, which incites a civil war (that was quick!). Bea and Quinn are able to separately escape the pod: Bea with the help of Alina and Silas' neighbor and Alina's parents (who were presumed dead!); Quinn with the help of his own father. At the end of the book, they arrive at the Grove and reunite. They discover that the Grove has been destroyed but Jazz (a child who lived there) is still alive and tells them that everyone has headed to the river and they set off to find them.