The Zeta Uprising was the rioting and revolution of the human prisoners on the alien mothership Zeta in the year 2277 in the orbit of the planet Earth. It resulted in a complete human takeover of the ship and the destruction of a mothership sent in to destroy the Zeta after the human hijacking.
Recon craft Theta crash-landed in the wilderness north of Minefield. The aliens then set up a trap in the area, using the ship's distress signal to lure wastelanders into the crash site in order to be abducted for their experiments. The Lone Wanderer was one of these individuals. After the Lone Wanderer awakened, they were locked in a cell with another abductee named Somah.
With a plan Somah drew up, she and the Lone Wanderer pretended to fight in order to spook the aliens and force them to enter the cell and break up the fight. They then attacked and killed the alien security and used their weapons to take over the detention wing. After meeting up with Sally, she helped the Lone Wanderer traverse the sectors of the ship, and assisted their path through the steamworks. Upon reaching the engineering core, the Lone Wanderer opened the cryo stasis chamber for Hartigan, a pre-War astronaut, in order to enlist his assistance in the uprising. His job was to traverse the ship's space walk and reach the bridge. However, he was dead upon exit. Therefore, the Lone Wanderer was responsible for traversing the space walk. Three other abductees, Elliott Tercorien, Paulson, and Toshiro Kago, were freed from stasis, and could have helped in the uprising.
The space walk could not be traversed, due to the levitation beam to the bridge being shut off by the aliens. Therefore, three generators had to be destroyed in order to open the door to the decompression chamber. The Lone Wanderer fought through the cryo labs, the robot assembly area, and the hangar, destroying each generator. The Lone Wanderer then put on the space suit and traveled the space walk, before reaching a levitation beam to the Observation deck
On the observation deck, the alien captain appeared on a hologram, and gave the rebels an unintelligible and rather useless monologue. Just as the hologram dissipated, the ship's death ray fired a warning shot into space in order to scare the rebels into surrendering. The Lone Wanderer then battled the aliens in the Death Ray sectors and deactivated the death ray gun. A shot from the death ray could possibly have been fired at Earth. The only obstacle left was the bridge.
At the bridge, the alien captain was killed, and immediately afterwards, a support mothership arrived to destroy the Zeta, since it had been hijacked by the human prisoners. By reactivating and using the ship's death ray, the support mothership was destroyed, and crash-landed.
A beacon was accidentally somehow sent from the ship, and it landed in what was once the wreckage of recon craft Theta. It therefore allowed the Lone Wanderer free passage to and from the Capital Wasteland to Zeta. Sally remained on ship, however, depending on if they survived, Elliott Tercorien would have remained on ship and took care of the ship while its new captain, the Lone Wanderer, was absent. Toshiro Kago would also have stayed. Somah would have returned to the Capital Wasteland, and Paulson would have left for an unknown location on Earth.