The show opens with a shot of Serenity flying by a planet, and then zooms into the ship and through its passages to end on River, who lies in bed listening to not-quite-audible voices. She arises and takes a walk through the ship's rooms and corridors, encountering her shipmates in varied conversations with each other. Simon is relaxing with Kaylee in the common room, telling her an amusing anecdote about medical school. River suddenly "sees" them looking at her, with Simon telling her that he'd "be there right now", implying she is responsible for taking him away from his successful medical career. She then finds Jayne and Shepherd Book in the kitchen, where she "hears" Jayne repeat his confession to Mal about selling out the Tams on Ariel, and Book mutter an angry but cryptic statement hinting at his less wholesome past. River continues to wander the ship, and is moved by the sound of ocean waves as Zoe and Wash passionately kiss on the nearby bridge. Above the cargo bay, as Mal and Inara discuss her impending departure, River sees their unspoken frustrations over their unrealized relationship. None of the people she encounters are aware of her presence - except when speaking directly to her - making it clear that this is River's mind "walking" telepathically through the ship.
Fleeing the intense emotions, River runs down to the unoccupied cargo bay, where she spots a tree branch. She sees herself on leaf-strewn ground and picks up the branch, telling herself "It's just an object. Doesn't mean what you think." Suddenly, the real world returns, and she finds that she is holding one of Jayne's pistols while the crew surrounds her in a panic, trying to get her to give up the weapon. Mal takes the gun from her and discovers it is loaded and ready to fire. When Mal admonishes her for handling loaded weapons, River runs off, crying.
As Mal comments on how alone they are, the camera cuts to a small vessel closing with Serenity, aboard which is a man reviewing wanted bulletins for Simon and River. Meanwhile, the crew discuss the dangers of River's presence on the ship. When Zoe muses whether River has ever handled a gun, Kaylee reluctantly tells everyone about her experience during their assault on Adelei Niska's SkyPlex, when River killed three attackers with single shots with her eyes closed. The crew begin to speculate that River may be a "reader", having psychic powers, and though Simon objects, they begin to question whether she is a danger to them. While talking, the crew are being listened to: outside the hull of Serenity, the bounty hunter has left his ship and has tapped into the hull, and below the room, in the cargo bay, River is listening through the floor plating.
Once the crew goes to sleep, the bounty hunter boards Serenity. He first encounters Mal, quickly knocks him unconscious, drops him into his cabin, and then locks the rest of the sleeping crew in their cabins. He surprises Kaylee in the engine room, ties her up, and threatens to rape her if she does not cooperate. Next, he disables Book with a surprise attack. Simon hears a noise and rises to check on his sister, only to be attacked by the stranger, who addresses him by name. The bounty hunter, Jubal Early, waxes philosophically on the nature of things while he demands to know where River is. Though Simon refuses to help Early, the bounty hunter threatens to kill him and rape Kaylee if he refuses, and the doctor reluctantly agrees.
With Simon accompanying him, Early checks out the cargo bay and shuttles. When Inara tries to appeal to Early's emotional side, he smacks her across the face, and then locks her in her shuttle. The two men finally arrive on the bridge, where Early settles on a direct threat, announcing loudly to the ship that he will kill Simon if River doesn't reveal herself. River then responds over the ship's intercom, telling Early about how she was unwanted on the ship but could not bring herself to leave, so she simply "melted away", becoming part of Serenity.
In the engine room, River's voice comes over the intercom, reassuring Kaylee and asking her for help. On the bridge, Early is skeptical about River's claim, but she reveals uncanny knowledge of the bounty hunter's own weaknesses. Early gradually starts to accept the possibility that River has joined with the vessel. Meanwhile, River sends Kaylee, who has freed herself, to unlock the cabins. Zoe begins to prepare an assault, but River insists that they do not use guns, and instead tells Mal of an alternate plan.
On the bridge, River continues her conversation with Early, needling him about his violent tendencies and his past. Early realizes that River is not part of Serenity, but has managed to sneak onto his ship, which puts him on the defensive. River reassures him that she will go with him as his bounty, as she is a burden on her shipmates, and her departure will allow them to get on with their lives. As Early starts to leave, Simon tries to stop him, but in the process is shot in the leg. Jayne wakes up and pulls the curtain off of his weapons compartment, but just uses it as a blanket and returns to sleep. Leaving Simon in the cockpit, the bounty hunter starts his EVA back to his ship, but finds Mal outside, waiting in ambush. Mal shoves Early off into space, before welcoming River back aboard Serenity.
Later, in the infirmary, Simon instructs Zoe as she removes the bullet from his leg. Inara walks away from Mal as he tries to examine her cut lip. In the cargo bay, Jayne mocks Book's failure to defeat Early, despite "all them years of priest trainin'", and Book implies that he fought Early and only succumbed after a prolonged fight. Kaylee and River play jacks while Kaylee relates a racy anecdote from her past. River picks up and examines the bouncing ball, with its swirling, multicolored surface, which recalls the multicolored planet Serenity flies by in the opening shot. The camera pans down through and out of the ship to show Serenity sailing off into space.
The show ends on Jubal Early, tumbling helplessly through space, who says, "Well... Here I am."