We open with River in bed. She can hear people talking. She gets up to walk around. Simon and Kaylee are talking about his time at medical school. Simon turns to River and says, "I would be there right now." It appears to be some sort of flashback. Next she goes into the dining area where Jayne and Book are both talking. They both look at her and make a rude comment. Later it happens when she hears Inara and Mal talking. It appears that River is either reading their minds or it is what she imagines they are saying.
River sees a stick in the cargo bay, when she picks it up to look at it, everyone yells at once for her to put it down. Then we see it is a gun. Mal takes the gun and River runs away saying, "it's getting very crowded in here" and it is unclear if she means in Serenity, or in her mind.
On the bridge, Mal, Jayne, Wash & Zoe are discussing the River incident. Mal says they should bolt her door from the outside. Zoe points out that she's never picked up a gun before. Kaylee says that isn't so. Meanwhile, a man gets out of a small ship and quietly drifts to Serenity, and looks in the window.
Kaylee tells the story of how River shot three men with her eyes closed when they went to rescue Mal from Niska. As they discuss the River situation, we see River listening in another room. Outside, the guy on top of Serenity is also listening. Simon says that River is "deeply intuitive"; Mal thinks she can read minds. After some discussion, they break for sleep. Simon and Kaylee talk in the passageway and nearly kiss, but then Book walks past and the moment is lost. Mal is the last to leave the dining area, and turns off the light. A black man with a large gun and red spacesuit/armor comes down a ladder into the ship. Coming around a corner, he runs square into Mal.
After a quick fight, he gets the best of Mal, and tosses the Captain into his cabin. Kaylee is in the engine room and hears something. She is startled when the strange man appears right in front of her. The man seems to have a rambling semi-incoherent way of speaking. He asks Kaylee if she's ever been raped. He points out that no one can help her, and Mal is locked in his cabin. He forces Kaylee to tell him where River's room is.
The man next encounters Book on the way to the shower. Book is knocked out easily. He then surprises Simon. During the course of more semi-coherent rambling, he reveals that he is a bounty hunter named Early. He claims to have been tracking them since Ariel. Simon's resistance is broken when Early tells him Simon that Kaylee will suffer before she dies.
They continue looking for River. Early stops to lick a railing. He slaps Inara when she tries to reason with him. When they get to the bridge, River talks over the intercom. She tells Early that she wasn't wanted, so she disappeared and faded into space. Now she claims to be inhabiting Serenity. She appears to be able to speak to the entire ship at once and also to individual rooms. River tells Kaylee that she is in charge, and to cut her self free. Back on the bridge, River calls Early by his first name, Jubal. She tells him he likes to hurt people.
River contacts Mal and reveals she has a plan. Kaylee removes the lock from the crew quarters. River includes Wash & Zoe in on the plan. She tells a story about how Early killed a neighbor's dog when he was little, we get the idea that Early is not okay in the head, in case the earlier hints weren't enough. River tells Early that she will go with him voluntarily. Simon doesn't care for this notion and attacks Early, getting shot in the leg for his effort.
Early seems happy with the compromise and starts to head back to his own ship. "You made the right decision," he tells River when he gets outside the ship. It's Mal's turn to surprise Early. Mal is already outside in a suit. When he hits Early, the man drifts off into space, with no safety line. River drifts back down to Serenity where Mal catches her. For the first time we see someone other than Simon is clearly glad to have River on board.
In medical, Zoe has to operate on Simon to extract the bullet. She points out that she is much more familiar with putting bullets into people than taking them out. Life goes back to what passes for normal as Serenity flies away. The last thing we see is Jubal Early drifting slowly through space.