The
resources of Earth have been depleted, and humanity has moved to another star system and terraformed many of the planets.
All the planets are controlled by the supposedly peace-loving yet still rather authoritarian Alliance. But a frontier justice
still holds sway farther from the "core planets", where outlaws like the crew of Serenity can scrape out a living if they
keep clear of Alliance forces and the Reavers, savage and cannibalistic humans
who dwell beyond the outer planets and raid the Alliance worlds around the rim.
In
order to earn her continued passage onboard Serenity, a fugitive from the Alliance,
the telepathic River Tam (Summer Glau), accompanies Captain Malcolm Reynolds (Nathan Fillion), Jayne (Adam Baldwin), and Zoë
(Gina Torres) on a mission to steal the payroll of an outer planet security company financed by the Alliance.
During the robbery, the crew narrowly avoids capture by a Reaver raiding party when River is able to telepathically sense
their approach. Wash (Alan Tudyk), the ship's pilot (and Zoë's husband) brings
the ship to intercept the crew's surface vehicle, saving the crew from a grisly fate.
River's
brother Simon (Sean Maher), the crew's doctor, angrily reacts to the captain's willingness to put his younger sister in such
grave danger. Captain Reynolds responds by suggesting they leave at the next planet they land on, Beaumonde, where the crew
expects to sell their loot. Simon agrees to the arrangement. The Tams do indeed disembark at Beaumonde, but while the captain
haggles with the buyers, River suddenly starts attacking people in the same bar that the captain and Jayne are patronizing.
Despite being a 90 pound (41 kg) girl, she manages to incapacitate everyone, including Jayne, and is about to shoot Captain
Reynolds when Simon arrives and shouts a phrase in Russian, causing her to fall asleep.
Simon
explains to the captain that, during her captivity by the Alliance, she was trained
and conditioned to become an assassin. The only thing that can stop her after this conditioning has been triggered is the
"safe-word" he uttered. Despite knowledge of this new danger and his anger at not being told about the possibility of carrying
a potential living weapon, the captain allows Simon and River to continue travelling on Serenity.
The
crew contacts Mr. Universe (David Krumholtz), a reclusive techno-geek who dwells with his robotic wife on a planet surrounded
by an opaque ion cloud. After watching the security camera footage of the bar on Beaumonde, Mr. Universe discovers that River's
outburst was triggered by a subliminal message in a seemingly harmless cartoon advertisement that had been broadcast all over
the Alliance during the previous weeks. He tells the crew that before her attack, River had whispered the name "Miranda."
He also notes that the footage has been viewed by someone else with high Alliance
clearance.
Fearing
Alliance pursuit, the crew takes refuge in the Haven mining colony with Shepherd
Book (Ron Glass), a priest who once travelled with Serenity's crew. Book warns Mal that the Alliance
agent pursuing River is likely to be an "Operative," and very dangerous. Shortly thereafter, the captain receives a call from
Inara (Morena Baccarin), another former passenger. Their conversation is awkward but pleasant enough — with no arguing
— leading Mal and Zoe to the conclusion that it's a trap, but they decide to visit Inara anyway. Mal's fears are realized;
Inara is held hostage by a ruthless and nameless Operative (Chiwetel Ejiofor). The Operative offers to let the captain go
on his way if he turns River over to him, but thanks to Inara's quick thinking, she and the captain escape the Operative and
return to Serenity, which takes off undetected.
Another
of River's outbursts shows the crew the meaning of "Miranda". It is the name of an outer rim planet, which had once been inhabited
but was thought to be wiped out in a terraforming accident. River had subconsciously learned something mysterious about the
planet when she came in telepathic contact with a member of the Alliance Parliament during her training. Travelling to Miranda
to learn more would require crossing through what is now Reaver territory, which the crew members agree would be suicide,
so instead Serenity returns to Haven and Shepherd Book.
On
arrival, however, the crew discovers that the outpost has been ravaged by Alliance
forces, and its inhabitants killed. Mal finds Book, who has shot down the attacking ship. However, he has been mortally wounded
and dies in Mal's arms. Several other outposts that had harboured Serenity in the past have also been destroyed. Captain Reynolds
receives a message from the Operative claiming responsibility, and promising more of the same until River is turned over.
Mal
comes out and orders that Serenity be remodelled to look like a Reaver ship, which involves war painting and mutilating the
hull, making a dangerous modification to the engine, arming the weaponless cargo vessel with the settlers' cannon and tying
bodies of the dead settlers to the prow. Everyone protests, but Mal furiously informs them that they can either do what he
says or leave the ship now.
Serenity,
now painted red and looking far more menacing, leaves for Miranda. The ship moves through a whole mass of Reaver vessels,
and after an agonising wait, finally reaches the other side without incident.
Upon
reaching Miranda, the crew discovers a normal, terraformed planet, with an earth-like environment which is completely habitable.
The strange part is that the sprawling cities that dot the planet's surface are empty. Inside the buildings and cars are badly
decomposed corpses, with no apparent cause of death. There are no signs of violence or disease. It is as if the people simply
died.
The
crew discover a log recorded by an Alliance research and rescue team after the
disaster. The log recounts what has happened: the Alliance administered the chemical
substance G-23 paxilon hydrochlorate, or simply "Pax", to the populace. It was supposed to remove aggression and thus render
the planet free of violence. An unfortunate side effect was that the populace had stopped working, or eating, or caring about
anything. They simply gave up on life and died in their newfound non-aggressive state. However, there was a small minority
of the populace (approximately a tenth of a percent, thus given the planet's original population of 30,000,000 approximately
30,000 individuals) for which the drug had the opposite effect. They became extremely aggressive and mentally unstable, mutilating
their own bodies, and killing the researchers who had come to investigate. They eventually left the planet and formed into
the much feared Reavers. Thus, the Alliance was actually responsible for the creation
of this menace.
Everyone
is sickened by this revelation, but none more so than Mal. This was exactly the sort of thing that the Browncoats had been
fighting to prevent: the Alliance's belief that they can make people "better";
that everyone must conform to them, regardless of the cost or consequence. For the first time in years, Mal is moved by something
greater than himself; a belief, something he thought he'd lost in the Battle of Serenity Valley.
The
plan is to reveal this secret to all the worlds by using the transmitter equipment belonging to Mr. Universe. Unfortunately,
the Operative has predicted this, and is already waiting at Mr. Universe's headquarters, along with an Alliance
fleet. When just about to leave Reaver territory, Serenity opens fire upon a Reaver ship. The ensuing chase by all the nearby
Reaver warships causes the previously lone Serenity to emerge from Reaver space flanked by a large force of deadly Reaver
ships, while the Alliance fleet was waiting near the Reaver space with the intention
to destroy Serenity. There is a massive battle between the Alliance fleet and
the Reaver fleet, as Wash steers Serenity towards the planet with both the Alliance
and the Reavers trying to destroy them as well as each other. During the attack, the Operative's ship is destroyed, but he
flees the battle in an escape pod and follows the crew to the surface.
Serenity
is followed by a Reaver ship, which fires an electro-magnetic pulse at them, disabling power. Wash
is able to restore emergency power at the last minute and effect a crash landing. While Serenity suffers massive damage including
having one of its engines torn off, it looks like the crew is out of danger. As everyone begins to relax, a Reaver harpoon
suddenly smashes through the window, impaling Wash who dies instantly. Unfortunately
for Wash, the cockpit was the only point that the Reaver harpooners could attack
from the outside. There is no time to mourn and Mal pulls Zoë away from Wash's
dead body just as another harpoon is fired into the cockpit. Fleeing Serenity to continue their assumed mission of getting
the word out, the crew decides to set up a last stand in a small corridor to hold off the Reavers and give Mal the time he
needs to make way to Mr. Universe and transmit the message.
Mal
arrives to find Mr. Universe has been killed. However, before he died, he was able to leave a pre-recorded message with his
robotic wife which informs Mal that there is a secondary transmitter in another area of the complex. Meanwhile the crew is
losing ground to the Reavers and is forced to retreat when Zoë and Kaylee are injured. The Operative arrives on the planet
and runs into the robotic wife, who repeats the message, informing him where the secondary transmitter is. The crew try to
close the blast door, but it stops leaving a small opening. This buys them some time, but when the doctor is shot by a stray
bullet, there is no one to tend to the injured. He tells them he needs his medical bag which he left in the preceding room.
River leaps through the blast door, throws the medical kit back in, closes the door and is swarmed by the Reavers.
Mal
reaches the second transmitter and finds that it is inconveniently located on a platform surrounded by a large drop. He is
about to attempt to reach the platform when the Operative shows up. They have a stand-off, which results in Mal being quicker
on the draw and shooting (but not killing) the Operative. Mal then proceeds to try and reach the transmitter, but the wounded
Operative follows him. There is a fight between them with the Operative using a pressure point which is designed to completely
disable his opponent — it fails, and has no effect on Mal due to nerves severed in an old war injury.
Mal
does not kill the Operative, and instead disables him with a similar move and leaves him trussed up to watch the recording
from Miranda. Returning to the crew, he is informed that River was trapped on the other side of the blast door with the Reavers
— presumably killed. The door opens to reveal that, instead, River has killed all the Reavers. As she finishes, the
Alliance troops enter, but instead of giving permission to shoot her, the Operative
orders the squad to stand down.
After
the crew buries the bodies of their friends Mr. Universe, Shepherd Book, and Wash
on Haven, the crew patches up Serenity in a repair yard on the planet Persephone. Just as they are ready to leave, the Operative
makes his own exit, promising Mal they will never encounter each other again. In the payoff to a subplot from both the series
and the film, Simon and Kaylee finally make love. Zoe tells Mal that "she's tore up plenty, but she'll fly true," and Serenity
heads back into outer space, with Mal in Wash's seat at the helm, and River
acting as his co-pilot. The final shot shows the ship flying off triumphantly into the distance, until a random piece of metal
flies from the back of the ship and hits the camera, prompting Mal's final, inquisitive line of "What was that?".