The consequences of the Miranda broadcast unfold. Though the Alliance has been able to fool most of the worlds under their control that the Miranda broadcast was a fake, it has hit a patch of difficulty trying to convince the rim worlds of the same thing. A rebel movement, made up of former Browncoats who refuse to give up the fight aganist the Alliance, use this as an opportunity to start a second War of Independence. This is the same movement that helped Simon rescue River but for the reason of using her as a weapon aganist the Alliance, which Simon was opposed to and took her from their clutches before they had a chance to try.
At the capital of the Alliance, tensions are mounting between two sides of Parialment. One is under the influence of the Blue Sun Corporation and the other is aganist that influence. The leader of the anti-Blue Sun faction of Parialment starts receiving help from someone who wants to get rid of the Corporation, seeing it as the source of the Alliance's corruption. That someone turns out to be the Operative.
Meanwhile, the Serenity crew settles on a planet where Mal's mother lives. They plan on laying low there and get themselves a new living to get them by for the time being since most of their clients have been killed. Mal tries to give things a shot with Inara, who feels compelled to finally tell Mal that she is suffering from a terminal illness, which she has been able to keep it at bay with injections so far. Zoe struggles with her grief over Wash's death. Jayne starts questioning the direction of his life after the deaths of two of his crewmates. River falls for someone who lives on the planet and is drawn to that person when his mind is the only mind River can't read for some reason.
In the seventh episode, Simon feels the time has come for them to involve themselves in what's going off-world while Mal feels they have done enough with the Miranda broadcast. This splits the Serenity crew into two. Jayne, River, and Inara on Mal's side, and Zoe and Kaylee on Simon's side. By the end of the episode, Simon takes one half of the crew with him off-world while Mal and the other half stays on the planet.