Sometimes You Still Lose
Reach the bunker, locate Damien, gain entry into the central ctOS building.
Enter the bunker to watch a cutscene, then set course for the next waypoint to find Damien. You'll be interrupted on the way and be given a new destination: the central ctOS building. Take great care as you make your way to the new destination, as Damien has taken control of almost everything. Watch out for the red marker that indicates Damien is hacking something nearby, and be especially careful around steam pipes and bridges.
When you arrive safely at your destination, head to the south-east side to find a door next to the hacking point. Hack into the system to begin another hotspot minigame, but you'll discover shortly after you turn the first point that you're being locked out.
The puzzle is actually possible to solve -- you just have to be extremely quick. Start with the middle (lower-left) point and turn it once. Move to the point in the upper-left corner and turn it once, then unlock the other point in the middle (upper-right). Move back to the starting point and turn it once, then move back to the upper-left point and turn it once again. Now go back to the middle (upper-right) point and turn it twice, then move to the point in the lower left corner and turn it once.
Next move back to the starting point and turn it once more, then unlock the point in the lower-right corner. Go back to the starting point again for one last turn, then move to the lower-left point and turn it once. Turn the middle point (upper-right) three times, then the point in the upper-right corner once, and the point in the upper-left corner once. Turn the bottom-left point twice, then finally the upper-left point twice to unlock the final point in the middle, near the top.
Upload T-Bone's virus into the ctOS.
Damien is still in control of the ctOS and it's starting to interrupt your GPS. There are a dozen waypoints turning on and off all over the map, but you only need to access three of them. To determine which waypoints are real, pay close attention to the waypoint names on the main game screen. Most of them will be gibberish, but three names will read "Hack." These are the places you need to go, and coincidentally they're all ctOS centers you've already visited.
The police are hot on your tail, though, with both squad cars and helicopters in pursuit. If you can disable the helicopter and set off a Blackout, that will help, and you can also take advantage of Damien's control of ctOS. Drive over a bridge and Damien will activate it in an attempt to stop you, but all that will really happen if you're careful enough is that it stops the police. You can take advantage of steam pipes in the street in the same way.
Evade the police as best you can as you move between the three centers, uploading T-Bone's virus each time. Once the third virus is installed, it's time to go back to the central ctOS building and shut it down once and for all.
Shut down ctOS.
Things will return to normal after you install the virus. Head back to the hacking point at the central ctOS building and access the hacking minigame once again.
Start in the lower-left corner and turn that point twice. Move to the lower-left point in the center and turn it once. Turn the upper-left point once, then go back to the center and unlock the upper-right point in the center, then turn it three times. Unlock the point in the lower-right corner, then move back to the center area and click the upper-right point in the center section three more times. Turn the upper-left point once, then the upper-right point once, then head back to the center and turn the lower-left point in the center section once in order to unlock the final point in the upper-right portion of the puzzle.
Switch to the camera in the upper-right corner of the room, then hack the Intrude location directly ahead. Hit the top point in the hotspot, then shut down the system via the satellite.
Use a boat to reach Damien.
Go back outside and head down the stairs to the right to reach the boats waiting for you at the pier. Take a boat to the next waypoint, which is a lighthouse. When you arrive, head up the stairs and climb into the lift at the top to reach the level above. Head through the door and into the lighthouse.
Climb the stairs, then the ladder. Move around to the opposite side to find a ladder, then use it to reach the very top of the lighthouse for a cutscene. You'll be asked to hand your phone over, but instead you should perform a hack when prompted, then a takedown immediately after. Finally, put a bullet in Damien to wrap up the single-player story.
Walk away or shoot Maurice.
After the credits, you have a choice. Do as you see fit.