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1: You've uploaded the spec to the Illuminati. Chad congratulates you and tells you to destroy the Dentons and the machine in the statue. On your way out of the UNATCO HQ you'll find no resistance at all, until you exit the building and reach the West Side.
2: Just outside and up the ramp, a few PAP's and Saman await. Use your Spy Drone to take down a couple if you have it, else snipe at them from the back of the room or use your Mag Rail. Saman is the toughest but he merely takes a few more hits than the rest. When the battle is over, head to the South Docks, where the IEG's will be friendly to you. Exit to the Illuminati Encampment, head around the bunker to the door, and enter to speak with both Chad and Nicolette multiple times for their explanation.
3: Exit the Illuminati Encampment and head north just until you see all of ApostleCorp gathered around the entrance, including JC and Paul Denton, Grays and three Hunter Seeker bots. By far the easiest way I found to deal with them is to snipe from afar with silencer mod attached. A prime position is just around the corner from the UNATCO HQ building using the scope. Concentrate on the humonoids first, and they'll all simply scramble around not knowing which direction you are. When they're down, approach the Hunter Seekers and use whatever method you wish to disable them. Mag Rail alt-fire works great, as well as the Spy Drone.
4: Approach the Statue Entrance door, open it and back up to the small building. Again, using your sniper rifle (or rocket launcher), fire on the machine in the center of the room. The turrets and Grays inside won't bother you from this distance. When the machine is gone, you'll watch the ending! Congratulations on beating Deus Ex: Invisible War!