As a childhood River listens to her teacher in class, a moment of tension between the two reveals that it’s actually a memory that a 17 year old River is experiencing while she undergoes a treatment at the Alliance academy facility where she was held before her brother Simon had come to break her out. A man dressed in Alliance garb watches over the procedure as the doctor in charge explains the procedures they’re using, leaving the Alliance officer to mention that River always did love dancing. When the doctor looks confused, the man, revealed as being Simon in disguise, uses a piece of technology to knock everyone in the room out, and he and River manage to escape up a shaft where a ship awaits them.
Everything in the scene suddenly pauses, as an Alliance agent named the Operative pushes a button a viewing device, revealing the security footage from when the incident happened. The Operative then questions the doctor about what happened, and after learning that River had met members of the Alliance Parliament and possibly gained access to their deep secrets, he kills the Doctor’s staff with his sword, and uses a pressure point to paralyze the Doctor himself before allowing his frozen body to fall upon the blade, killing himself, as he heads off to begin his search for the Tam’s.
Meanwhile on Serenity, tensions flare up between Mal and Simon as it’s revealed River has been chosen to accompany the crew on their next job, a bank robbery in a small town on a planet in the outskirts of the galaxy. Mal’s reasoning is that they’ve been on the ship long enough for her to start earning her keep. The plan goes well at first but then River senses reavers approaching, leading to a quick escape and high speed chase which ends with Zoe piloting their mule escape ship into Serenity while both are still moving. Simon punches Mal for endangering his sister and the two have words, eventually mutually deciding that they will go their separate ways on the next planet.
As Mal meets with his clients regarding the bank job, River wanders into the bar and becomes transfixed by a commercial playing before suddenly attacking everyone in the bar. Chaos ensues and only stops when Simon appears and utters a safe word that causes River to fall asleep instantly, enabling Mal and company to get her back to the ship, where Simon explains that River was trained to be an assassin.
They seek out the help of a computer genius named Mr Universe who hacks into the security footage, noting that River said one word before stating the fight: Miranda. He also lets them know that no official report was filed about it and that the footage was hard to obtain as well, both odd occurrences. Fearing Alliance pursuit, Serenity heads to Haven, a safe planet of sorts where Shepard Book has taken refuge, and welcomes them in with open arms, albeit wondering why Mal saved the Tams yet again.
Inara contacts Serenity, asking them for their help, which they immediately recognize as having the tell tale signs of a trap, yet still go. Mal finds Inara and is immediately attacked by the Operative, only managing to get away from him when Inara’s incense actually turns out to be a weapon that causes a distraction and provides cover for their escape.
As the crew heads back to Haven, a locked up River escapes and begins knocking out members of the ship, including her own brother, fearing he will use the safe word again. Eventually she gets to the cockpit and reveals what Miranda means: a reference to a planet far out in the outer reaches of the galaxy, near Reaver territory, a forgotten planet shrouded in mystery where the normal terraforming practices had apparently failed and was left abandoned.
Serenity returns to Haven only to find that the entire community has been attacked and slaughtered by the Operative who contacts Mal, informing that all of his safe havens have been similarly attacked. Mal makes the decision to disguise Serenity as a reaver ship, using red paint, left over weapons, and the dead bodies around them to fulfill the illusion. Luckily, wash manages to get them through Reaver space unscathed and they touch down on the planet.
As they witness dead bodies everywhere they realize a key difference: all of the bodies show no signs of distress or violent death or pain, instead they just seem to have stopped living, laying down to just die. An old recording is unearthed which reveals that after the planet was successfully terraformed, the Alliance conducted experiments on the population to see if they could control them and remove all aggression, using airborne drugs that caused 90% of the population to become extremely apathetic, eventually not caring about anything, including their own survival, which in turn caused their deaths. The remaining 10% responded inversely to the drug, becoming enraged and cannibalistic, eventually transforming into the race known as Reavers.
Armed with this evidence, Mal plans to head back to Mr Universe and use his broadcasting tools to get this information out to the entire Verse so they can see the truth behind the Alliance’s past. As they begin their return flight through Reaver space however, they end up being attacked by a Reaver ship but luckily Mal had prepared for that and they manage to get away.
Upon arrival at Mr Universe’s station, they are greeted by the Operative and a huge armada of Alliance ships. The Operative’s gloating is short lived however as Serenity is followed by all of the Reaver ships that were in the area and a huge battle ensues which enables Mal and crew to slip through and land, despite losing control of the ship due to an EMP from the Reavers. That victory does not last long however as a harpoon from a Reaver ship punctures the cockpit, killing Wash instantly.
The rest of the crew escape and enter Mr Universe’s complex, and set up in an area where they can easily defend against the Reavers to allow enough time for Mal to get the information sent out. Mal enters and finds Mr Universe dead in the arms of his robot wife who has a prerecorded message he left for Mal that tells him there’s a backup broadcasting station below. Mal makes it there and begins to set up the broadcast but is attacked by the Operative who also managed to escape from the space battle. They fight, with Mal holding his own until the Operative uses the paralyzing move he used on the doctor. As the Operative relaxes, Mal recovers and manages to overpower him with a throat punch and secures him to the railing with his own sword, explaining that that particular nerve cluster was removed after the war, rendering him immune to the attack the Operative had used. Mal sends the broadcast out to the universe while the Operative comes to realize the magnitude of the atrocities he committed while fighting for the Alliance’s lie of a perfect universe.
Meanwhile, the Serenity crew, pushed back further by the Reavers, are dealing with Zoe, Kaylee and Simon all being injured badly. River runs out to the main passage, tosses back Simon’s med kit and locks the door behind her and begins attacking all the Reavers herself. As she defeats them all easily, Alliance troops rush in and surround her but the Operative tells them to stand down.
The crew hold a funeral for Wash and Book and return to their repaired ship, courtesy of help from the Operative who promises he won’t ever see them again, and River takes her place as Wash’s replacement pilot, with Mal nicknaming her little albatross, a symbol of good luck, while Serenity flies off through space as a piece of the ship falls off prompting a nervous exclamation from Mal.
Shiny Trivia: