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The occupation of Omega gave Cerberus a huge strategic advantage during the Reaper War, bolstering their mobility throughout the Galaxy. Cerberus would overuse the mining facilities of Omega, pushing the mining equipment of the asteroid to its limits. Cerberus had difficulties maintaining the occupation, however. The Talons gang led by Nyreen Kandros is one of those groups still able to resist the occupation. In order to contain the civilian population, General Oleg Petrovsky erected large energy-intensive force fields throughout the station along with a large number of mechs and troops to maintain order.

Cerberus also conducted experiments with the Reaper-based adjutants in Omega. Initially this proved to be disaster. Large sections of Omega had to be shut down and sealed at a great cost of lives to contain outbreaks of uncontrolled Adjutants. Further experimentation would give Cerberus a full control of these creatures.

Aria begins her campaign to liberate Omega from Cerberus, having enlisted Commander Shepard in the process. Traveling aboard a captured Cerberus cruiser in order to infiltrate the Cerberus fleet surrounding the station, Aria opens her attack with a crippling blow to the fleet's flagship as her own fleet charges in via mass relay. The tables are soon turned, however, as Petrovsky reveals Omega's upgraded defenses by proceeding to inflict heavy damage on her fleet.

The initial invasion force lands on the station in escape pods. Aria and Shepards first disable Omega's defenses in order to give the invading fleet a chance. Later, with the help of Nyreen Kandros, they fight their way to Aria's Bunker on Omega's D-Deck, where Aria decides that in order to get to Petrovsky's command center in Afterlife, she needs to rally the Talons gang to her cause to supplement her ground forces, and disable the force fields that Cerberus has set up.

Cerberus is siphoning power for the force fields from one of Omega's main reactors deep within its mines. As access to it is mostly cut off by the force fields, Aria devises a plan to go through a powered-down eezo processing plant. Navigating the mines, Aria notices the machinery's overworked condition and estimates a month before they give out if the current trend continues.

Aria and company eventually reach an elevator to the reactor's back door, although General Petrovsky traps the squad in more force fields in anticipation of the move. Aria is not to be outdone, and forcibly opens a hole in the barrier for Shepard to pass through and disable the reactor.

Petrovsky dishes out another difficult dilemma at the turn of events: immediately shutting down the reactor will cause loss of life support in a lot of Omega's areas, which translates to loss of civilian lives. Shepard disables the reactor and ends the forced internal blockades.

With the Talons recruited, the populace incited, and the force fields down, the true war for Omega begins as the civilians revolt against Cerberus. Aria and Shepard prevent Cerberus from destroying Omega by blowing up the station's central support column, then join in the offensive to Afterlife from the Gozu District. Nyreen, who had been leading a separate assault with her Talons, sacrifices herself to kill a group of rogue Adjutants. Enraged at Nyreen's loss, Aria charges into Afterlife ahead of Shepard. However, due to the actions of Roman Shepard, Nyreen was saved from certain death.

Afterlife has been repurposed by Petrovsky in the course of making it his base of operations: the General traps Aria in a stasis field at the center of the establishment, powered by generators positioned at the corners. Shepard breaks her out and defeats all the Cerberus forces in Afterlife.

Defeated, Petrovsky surrenders himself and orders his troops to stand down, but Aria and Shepard decide whether he should be spared or executed on the spot. With Omega hers to rule once more, Aria announces its liberation to the citizenry, and vows to never lose the station again.

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