Almost immediately after his conversation with River at the end of the BDM, Mal goes to Inara's quarters and they finally become lovers.

It turns out that this is not the first time they have been physically intimate. A vengeful Saffron had forced this on them as punishment for having been left in the trash. Their relationship has been shaped by this event, making it near impossible for them to become emotionally close.

To compound this, even once they have become lovers, Inara continues to hide the knowledge that she is fatally ill from Mal until finally she has a seizure in front of him. In treating her in the aftermath of the seizure, Simon discovers that Inara is not sick but has been damaged by the treatment she has been receiving while on Sihnon and since.

With the discovery of Inara's condition, Serenity's post-BDM wanderings are directed not just by the need for work but also in order to find a cure for Inara. After a conversation with Simon, Mal believes that Saffron may be the key: while working as an ER doctor during his training, Simon on several occasions treated an ex-cop who used to tell wild stories about an infamous criminal organization called Betta Korski. Part of the operation included human trafficking and blackmail of important figures on Londinium. During their temporary kidnapping by Saffron, Inara accused her of being a Betta Korski-trained prostitute, which Saffron did not deny. Simon had been told by the ex-cop that Betta Korski abducted their recruits from the ranks of the Guild's Companions. Mal wants to find Saffron as a way into the world that hurt Inara, but Inara disagrees.

While Mal is preoccupied with his relationship with Inara and the need to heal her, Zoe finds the crew work that takes them to Highgate. The crew eventually discover that they have been hired by an idealistic but effective settlement of young core exiles, themselves outlawed by the Alliance. Their aim is to build Rim communities that will some day be able to challenge the Core. They have heard rumors about Serenity and Miranda and have used hiring the crew as a pretext for drawing them into their struggle. This means helping them establish their next settlement, on a planet called Cornelius.

Among the revolutionaries is a boy who has, like River, been broken out of an Academy. Both sides see that the other might help them in finding out what happened at the Academies. At the same time, Zoe is impatient to get on with the job at hand. She reproaches Mal, accusing him of going on one quest after another. Fearing that Zoe blames him for Wash's death, Mal lashes out at Inara, and Inara leaves Highgate for Sihnon. Having refused Mal's suggestion of searching for Saffron, she now plans to seek answers to her 'illness' and a cure herself. Zoe, too, leaves, intending to visit Wash's family on his home world.

Mal returns from Cornelius and finds himself in the middle of an Alliance attack: a tracking device had been planted on Serenity while she was being repaired at the end of the BDM. Lacking any other form of defence, Mal and the Academy boy turn Serenity into a bomb that takes out the Alliance ships. The Alliance attack has not been authorised centrally: it has been planned and driven by a rogue leader who has been cut loose by his superiors. He wants to make his men's sacrifices during the BDM mean something, particularly those who have been infected by the Reavers, and determines to kill the Tams. He comes close to achieving this but is shot by one of his own men who thinks this goes beyond their mission.

Inara finds out who has betrayed her on Sihnon and takes refuge in a Buddhist convent. The evil mastermind in whose web she has become entangled remains at large. Unable to wave Serenity, she contacts Mal through a shop in Highgate. They are reconciled, though neither makes a concrete promise about the future.

In the aftermath of Serenity's destruction, the crew seek a way forward. Kaylee realises that Simon will go wherever River goes and makes other plans; Jayne remains on Highgate for want of an alternative. The revolutionary settlers plan to move on to their new settlement on Cornelius and in the meantime try to strike a deal with the people living on Highgate about a valuable mine they have discovered. In everybody's minds is the Alliance, who are bound to be attracted to this mine, should they ever become aware of its existence. The remnants of the Alliance force ally themselves with the revolutionaries, though their main intention is to get back to their Reaverised companions, who have been abandoned on the planet shown at the end of the BDM. Mal acts as a fixer, working for a resolution that satisfies everybody, while his personal plan is to go to the Abbey on Persophone where he hopes to follow up a clue about Saffron and redeem his re-awakened soul.

And now - read on!