ACT 5 - Mission 01: Sometimes You Still Lose
Note: Fill up on everything before starting this mission as you won't have time to pick up anything during it.
Objective: Reach the bunker
Fast travel to the bunker and head inside for a cut-scene. Looks like everything is about to hit the fan. Leave the bunker and cross the bridge off the island.
Objective: Locate Damien
Great, Damien is now in control of all of Chicago. First Aiden needs to track him down before he can confront him. T-Bone will suggest a method for locating Damien, but it isn't going to be easy.
Objective: Gain entry into the central ctos building
Head to the marker on the map to find the building deserted. A marker will appear inside showing you where the access panel is. Head towards it and hack in. After a couple of attempts, Aiden will realize this is one computer he can't hack. T-Bone will propose a new way of doing it with one of his homemade viruses. But to infect the system, Aiden will need to travel to three points in the city to infect them first.
Objective: Upload T-Bone's virus into ctos
Note: Memorize the locations of the three infection points, as events will soon make your mission markers useless.
Head out of the building and head to each point in turn. The main difficulty of this mission is this objective. When Aiden approaches each point, a police scan will instantly be triggered and will continue until he is found. To upload the virus at each point, Aiden needs to stay at that location for a set amount of time. This means you will have to deal with a high level police pursuit at every point (although jammers can get you out of it once or twice with clever use).
Essentially you will need to use all the skills you have been honing the entire game to reach each point, upload the virus and get away successfully. Complete this and you will definitely be deserving of watching the final confrontation. Once again, there is no easy solution or strategy to getting this done.
Objective: Shut down ctos
After all that, head back to the ctos central building and try the panel once more. This time, on the way you will be contacted by DeadSec. Listen to Aiden's conversation and then hack the access panel. After pipe dream, you will be inside the central server room. Hack the server for one final pipe dream puzzle and Aiden will be soaring over Chicago. Hold down X (Xbox) or Square (Playstation) to turn off ctos.
Objective: Use a boat to reach Damien
Damien is on a lighthouse offshore, so head for the marker. Grab a boat along the way and make a beeline for the lighthouse. Several basic climbing sections later, you will be facing off against Damien in a final cut-scene. Near the end, events will happen and Aiden will enter focus mode a final time. Follow the prompts, the game and the cut-scene will end. Congratulations on beating Watch Dogs!
Watch the end credits and wait to the end of the first set of credits for a little bit extra, story-wise and to get your final achievement/ trophy.