The Alliance fleet was originally in orbit of the planet tasked with capturing the Serenity, in order to prevent Malcolm Reynolds from delivering the Miranda Message to Mr Universe for broadcast over the Cortex. Unknown to them, Mal had lured a fleet of Reaver ships after him, which promptly attacked the Alliance forces as well as continuing to pursue Mal's ship.
In the ensuing chaos, Serenity was able to slip past the blockade and penetrate the planet's atmosphere. It was pursued by a Reaver ship that eventually was able to hit it with an EM pulse that forced a crash landing. Only Wash's superior piloting abilitiy saved them from certain destruction.
Wash was able to bring Serenity down mostly intact at the entrance to Mr. Universe's home, though the ship was badly damaged. The Reavers followed, and killed Wash by shooting a harpoon through the ship's forward windscreen. The rest of the crew ran for the relative safety of Universe's bunker.
There, the crew found Mr. Universe dead and his equipment destroyed, but he had survived long enough to record a message in his love bot informing them of the location of a backup transmitter. Zoe and the rest of the crew volunteered to hold off the Reavers to allow Mal a chance to get to the transmitter and broadcast the recording.
Mal moved deeper into the facility while the others put together a makeshift barricade at a strategic location. The Reavers attacked in large numbers, and it was soon apparent that they would not be able to hold. Zoe suffered a critical wound to her back that exposed her spine, Kaylee was hit by a poisoned dart, and Simon was shot.
The crew retreated into a corridor and attempted to seal shut a set of blast doors to hold off the Reavers, but the mechanism to do so was outside with the enemy. River leaped through the door and closed it, trapping herself with the Reavers.
While this was happening, Mal located the transmitter and was preparing to send out the recording when he was again attacked by the Operative, who had survived the space battle as well. A vicious fight ensued. Mal barely emerged the winner and sends the wave, forcing the Operative to watch it as well.
The blast doors began to open, and the crew, prepared for it's last stand, was shocked to see a blood and gore drenched River standing alone in the doorway. At that moment, the wall behind her exploded and Alliance troops rushed in and surrounded them. They requested permission to fire from the Operative, who told them to stand down, ending the hostilities.