Hester Shaw is the protagonist.
When she was around eight years old, Valentine was good friends with Pandora and always treated Hester kindly until the day that Pandora and Valentine both found something that Pandora knew Valentine wanted for his own dark purposes. They fought over it, and Valentine stabbed Pandora in front of Hester and slashed Hester's face when she tried to save her mother. Before dying, Pandora gave Hester a necklace with an eye symbol, and Hester escaped.
After running away as a child, Shrike found her and raised her for years like his own. He had always noticed how sad Hester was, and he offered a solution to make the pain go away. Shrike revealed a robotic body he made for Hester, so that she can die and be reborn as a machine with no memory of the horrors of her childhood. She almost took him up on the offer until she heard about Valentine being close, so she headed off to hunt him down and left Shrike alone and angered by her deception.
After six months, Hester left to carry out revenge against Valentine, finally making it aboard London, where Valentine led the Guild of Historians. There, Hester posed as a refugee from Salzhaken and tried to stab Valentine, but Tom Natsworthy blocked the blow and chased her through the Gut. In order to escape, she jumped down a waste-chute leading out of the city. Valentine then pushed Tom after her.
After a few days wandering through the Out-Country, a desolate area entirely inhabited by Traction Cities, Hester and Tom came across Scuttlebug, a town. At the slave market of Rustwater, Tom and Hester were rescued by Anti-Traction League agent Anna Fang. During the chaos, Tom and Hester are pursued by Shrike, whom Hester revealed she knew.
Hester and Tom traveled with Anna to the airborne city Airhaven. There, they met with other members of the Anti-Traction League. Shrike catches up with them and Airhaven was destroyed in the ensuing fire. Following a fierce skirmish, Shrike was fatally wounded, realising that Hester was in love with Tom. Before perishing, he made peace with Hester and freed her of her promise. Hester, Tom, and Anna then travel to the Shield Wall with the surviving Anti-Tractionists.
At the Shield Wall, Hester and Anna manage to make it to London and head to St. Paul's. Hester finds that her mother's necklace holds the crash drive containing a kill switch for MEDUSA. As Valentine and Anna engaged in a duel, Hester proceeded to shut down MEDUSA with a crash drive before the final blast can fully take the wall down. She then pursued a fleeing Valentine to his airship, where the Historian revealed to her that he was her father, having been in love with Pandora before her death. When Hester has a chance to kill Valentine, she chooses not to. She hops on the Jenny Haniver with Tom who then brought down Valentine's craft, sending it crashing to the ground only to be crushed. They decided to travel in the Jenny Haniver to see the world.