This headquarters is located on the southern island area of the Albany map. Approach from the north and find the sole bridge leading across. Use the fallen tree stump to its right and use this to reach the guard tower on the headquarters’ side of the river. Kill the sniper here.
Jump to the next rooftop and at the far end drop down and kill the guard with the British hostage. Free him to complete the first objective. Continue south and climb the next guard tower. Again dispatch the sniper. This time, use the rope to reach the adjoining building’s roof and at the far end hop across to the flag. Interact with it to cut it down. Keep moving and kill the next sniper to the north.
Now we just need to enter the green search area and activate eagle vision to find the guard and then take him down. Use the rooftops as a vantage point to accomplish this much, much quicker and air assassinate him to take over the headquarters.