So: we don't exactly pick up where we left off in Pure. We ended Pure with Pressia, Partridge, Lyda, El Capitan, Illia, and Bradwell at Ingership's house. But fast forward in time a little bit — Bradwell, El Capitan, and Pressia are at OSR Headquarters, and Partridge, Lyda, and Illia are being looked over by the mothers.
At this point, OSR isn't a cruel organization anymore; it's been transformed into a will work for food sort of thing, where El Capitan provides food and shelter in return for people's services. Basically, El Capitan is building an army while Pressia and Bradwell are trying to figure out more about the Dome.
Bradwell found black boxes at Ingership's farmhouse, and they all store information about the world. Yeah, like the whole world: there are just tons and tons of facts. But there's also a black box that Bradwell named Fignan that he can't open—he assumes it holds some kind of different information.
Meanwhile, back with the mothers, Partridge and Lyda are being kept safe. But the mothers don't exactly like Partridge because he's male, so he doesn't get to do much. Lyda, on the other hand, has been trained to be a fierce warrior like the mothers.
So here's what happens: El Capitan stumbles upon a bunch of people who worship the Dome, and they tell him that there's The New Message. A child has been "made pure" by the Dome, and she carries a message that asks for the wretches to send Partridge back to the Dome. Either they comply, or the Dome starts murdering people.
Meanwhile, Bradwell and Pressia figure out that Fignan stores all of Ellery Willux's secrets after they unlocked Fignan by reciting all seven members of The Seven.
Partridge and Lyda get to work on maps of the Dome in a subway car (one of their temporary homes), and they are at this point deeply in love. Bradwell, El Capitan, and Pressia travel to find Partridge though, because they need to tell him about The New Message. They meet up, and Partridge realizes he needs to give himself back to the Dome to save everyone. He needs to "lead from within," and stop his father (who is dying) from finding the reversal to Rapid Cell Degeneration.
But of course, Special Forces come to ruin their day, and the whole gang gets in a royal rumble with them. Eventually, Partridge and Lyda are able to escape to an abandoned house where they have sex — Lyda ends up staying with the mothers later on, while Partridge gives himself up to the Dome.
Bradwell and Pressia escape the showdown, but El Capitan has a near-death experience with a remote spider-bomb. Luckily, his brother Helmud is able to dislodge the spider from El Capitan's leg and save the day. Bradwell and Pressia also have a near-death experience after almost drowning in cold water, but it's all good… they're totally in love at this point and save each other.
Back in the Dome, Partridge has been confined to a house with fake surroundings; it's a lot like the rehabilitation center that Lyda was confined to in Pure. He then meets his new stepmother, Mimi, and his new stepsister and fiancé, Iralene. The problem is that Iralene and Mimi are much older than they look; they are cryogenically frozen in capsules so that they can stay young. All of this was planned by Ellery Willux. Oh, and Iralene is completely cuckoo… which scares the heebie-jeebies out of Partridge.
Going back to the gang outside the Dome: they all figure out that the formula that Willux is searching for can be found in Newgrange, a Dome in Ireland. The only way to get there, though, is by airship. Conveniently, Willux hid the only unguarded airship in the Capitol Building, because he figured no wretch would make it there alive.
And what do you know, the gang makes it there alive, and El Capitan actually understands how to fly the thing.
The gang crashes the airship in Ireland just miles away from Newgrange. El Capitan gets a concussion and accidentally tells Pressia that he loves her, which creates a whole new dynamic between the three (since Bradwell also loves her).
Oh, and at around the same time Lyda finds out she's pregnant. And Partridge? He gets his memory erased by the Dome so he doesn't remember anything from his escape. Things are going fantastic.
But have no fear: Bradwell and El Capitan kiss and make up, and Pressia is able to retrieve the formula from Newgrange. And with the help of Iralene (who is much smarter than she appears), Partridge is able to figure out what happened to him before they erased his memory. He doesn't completely remember, but he finds a piece of paper he wrote before surgery that outlines everything that happened. His last mission is to kill his father.
The book ends with three key events: Pressia find Bradwell and El Capitan being killed by vines of a tree; she frees them both. El Capitan is okay, but Bradwell is pretty much dead. And since Pressia can't bear to see him die, she injects his birds with the serum from her mother's vial. All the sudden he has gigantic wings and has been pretty much been turned into a monster.
Lyda, on the other hand, escapes from the mothers—who have waged war against the Dome (but in particular, men). Our Good Mother has vowed to kill Partridge, so Lyda gives herself up to the Dome. She wakes up in the rehabilitation center in a ward close to Ellery Willux's. Partridge sees her before he meets with his father; he mostly remembers who she is and he leaves her a gift (a paper snowflake made from his list of memories), then he goes into his father's ward. He hesitates, but then decides to kill his father by poisoning him.