There are 10 gang headquarters: 6 in New York, 3 in River Valley and 1 in North Atlantic. They become available during Memory 3 Sequence 1.
To capture them, you must perform several tasks including: kill the gang leader, cut the flag, sabotage the poison supply, rescue British prisoners, etc. Benefits of capturing these gang spots include: adding a fast-travel point, synchronization of the area on your map (adding more events & collectibles), bank and fleet access.
Be more careful during capture, as enemies deal more damage than normal. Completing the capture without open combat will net you an extra money bonus. The gang leader likes to hit/shoot & run, dropping a gas bomb in your path. It is recommended you use the Assassin Killer outfit which has a permanent gas mask.
The game puts dots on the Gang HQ map icons to denote difficulty. 1 = easy, 2 = medium, 3 = hard. (*) asterisks below will substitute for the dots:
New York
1. Greenwich * (story-based)
2. King's Farm **
3. Lower Manhattan **
4. Waterfront ***
5. Stuyvesant's Farm ***
6. East Village ***
River Valley
7. Albany *
8. Two Bends **
9. Lac Eternal ***
North Atlantic
10. Halifax *