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Prior to Warlords of New York
During the initial outbreak, a large part of the Lower Manhattan region was turned into a Decontamination Zone (colloquially known as a Dark Zone, or DZ). As was standard with other Dark Zones, large walls were erected around the region, and travel to and from was minimized to Division agents and JTF personnel.
Months after the outbreak, the Lower Manhattan Dark Zone had subsequently lowered in threat level. The JTF decided to reopen the Dark Zone and set up a Base of Operations in the New York City Hall and a trading post in Wall Street Stock Exchange; meanwhile, some civilians and former JTF had formed a settlement called Haven, calling themselves the Peacekeepers. Lower Manhattan eventually became the safest place on the whole island ever since Midtown Manhattan became more volatile from hostile activity. However, the temporary peace that fell upon the city was shattered when Rogue Division agent Aaron Keener arrived, and organized a coordinated attack at the JTF and The Division.
Events of Warlords of New York
After the attack on the JTF headquarters in City Hall, Aaron Keener and his Rogue Lieutenants caused chaos in Lower Manhattan. Javier Kajika kidnapped, tortured, and killed many members of both the Peacekeepers and what JTF remained in the city with the help of the Cleaners. Vivian Conley lead the Cleaners to shipwrecked oil tanker and used the supply to further produce fuel for their flamethrowers. James Dragov lead the Rikers to take over the Stock Exchange, and ordered them to help protect Theo Parnell. Theo was the primary architect of the Rogue Network, and completed it while stationed in Lower Manhattan. Agents are called in from both Washington, D.C. and the nearby area. These agents, notably including Agents Alani Kelso and Faye Lau, wage a campaign against Keener and his lieutenants, culminating in a final showdown on Liberty Island. This battle ends with Aaron Keener dead, and the subsequent activation of the Rogue Network. After this, it is revealed that prominent Division Agent Faye Lau has gone rogue and sided with the Black Tusk. These events lead on into the first season, Shadow Tide.