How to capture a region
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On pirate-controlled region, players start with a huge disadvantage. All the territory -- towns and towers -- are controlled by the enemy faction. It takes a while to flip this balance in the player's favor, but there are some things you can do to help.
Bring colonists with you. This will let you establish a town, giving you +1. Before sailing into this region (and I mean sailing, not fast travel!), right-click allied ships to hire them. They will follow you and generally assist you. You are unable to directly assign them orders to attack or guard, they will simply follow along and assist when in range. Buy a guard tower kit, which are sold at colonies under the items tab (or bring a guard tower quest with you), and as soon as you establish or cap a town, plop down the tower. If you have Improve Structure, buff it, it will be much more powerful. Place the guard tower with some care. Too close to the town (overlapping captures circles) means that both town and tower can be captured simultaneously. There is also the possibility of reducing a town's growth potential. Make sure to start at the edges of the map, and build towers at choke points. Don't worry about the gold cost, you should be getting plenty just from clearing pirates. If you have the gold, bribe large pirate ships. Kill small ones. If you don't have gold for guard towers, at least place lighthouses near your towns. They will give your allies sight of the area. Don't hog all the allies. Sure, it's nice to have followers, but it also means they won't be able to roam the region and defend your lands on your own. If all else fails, lower the challenge a bit. Some regions are just innately more difficult than others.
Note that all of this assumes challenge 100%, damage 100%. Any more than that, and you're playing hard-mode.
In regards to the spawn count...
1 town = 3 ships max 2 towns = 4 ships 3+ towns = 5 ships
This *includes* the player -- so with 1 town you will only have 2 allies max! This is why bribing is useful. In Game slash commands
/team <message> : Send a message to your faction only. /global <message> : Message everyone on the world. /pm <player name> <message> : Message specific player. /ignore <player name> : Ignores a specific player. /ignore global : Ignores the chat box. /ignore join : Ignores join messages of other players. /anon : Enables and disables the anonymous mode. /info : Shows your SteamID. /who <player name> : /stat <player name> : Show player stats (only works on player's in current region). /obs <RegionID> : Watch the AIs or other players in specific region. Possible to control AI's by right-clicking and selecting control. /fps : Show framerate /resetChat : Reset Chat window to defaults. /report <text> : Message will be visible to all admins and be saved in the server's log file. /report <player> : Message will be visible to all admins and player information will be saved in the server's log file. /bug <text> : Message will be visible to all admins and be saved in the server's log file. /log <text> : Save text into your own local log file (My Documents\Windward\log.txt). /rep : Check your Faction Standing. /set kingRequirement = <number> : Set the number of players required for a Pirate King to appear in Heroic instances.
Additional Game Controls
Alt + Z : Hide user interface.