As soon as the plugin starts, you'll receive an incoming message. This message will allow you to set your initial relationship with the pirates. Notice that the reputation evolve slowly and you will see from time to time a pirate attacking you no matter your current standing toward the pirate community (it's a game engine limitation). It's sadly a game game engine limitation. This said, don't forget to double check your Friend/Foe settings from to time ;)

You can set your standing to Enemy. Your relation will be set to -50.000 points. All pirate ships except those handled by the Pirate Guild itself will be red. You can try to increase your standing by helping pirates through ECS. Or you can start to hunt PG ships as the police will give you additional money for the destruction of guild members (by any of your ships).

You can set it to Neutral. Your reputation will be set at 0 points. All pirates will be neutral to you. Attacking too much pirates will easily make them angry, though.

And if you want to be a pirate and do not worry about some pirate captures from time to time, set the option to Friendly. You'll get a reputation of 50.000 points. All the pirates will know you as one of them. You will also be automatically set as a member of the Pirate Guild.

Relations with the pirates in this plugin work like this :

+------------+---------+---------+-----------+---------+------------+------------+
| -1.000.000 |  Enemy  | -10.000 |  Neutral  | +10.000 |  Friendly  | +1.000.000 |
+------------+---------+---------+-----------+---------+------------+------------+

When pirates are your enemies, most of the ships (if not all) will be show as red. However, vessels owned by the Guild will stay neutral unless you've also attacked Guild's assets. When they are neutral, you'll find both hostile and friendly pirates. Finally, when they are friendly, most, if not all, pirates will be blue, even those you've attacked earlier may return to a neutral state after a while. You'll loose reputation points by killing pirates, and even more points if the pirate is affiliated to the Pirate Guild. You'll gain points by helping attacked pirate (through the comm. system, see next). Killing targets of the guild will also gives you points (and money). Being a member of the guild also slowly increase your standing, but you'll need at least 1.000 reputation points to join.

Communication between the playership and the Pirates is done via the ECS library. Target a pirate ship or a pirate station at less than 8km of your ship and press the keyboard shortcut assigned to the ECS library to comm with it. How the pilot/station will react depend of your guild rank and your general reputation with the pirate faction. The basic communication options allow you to ask a ship for the location of the nearest pirate base, to ask for an escort, to surrender, and more. You're also able to help a pilot when he is attacked by the police or military forces. The ECS system is very important and it is used for all interactions between the player and the plugin, so you'd better get used to it ;)

• It's not needed to restart the game. But, if you want to be a pirate, I think you should restart anyway, as the game will be much more enjoyable for you, especially if you're using both Pirate Guild and Yaki Armada. I'd suggest you to start with the “Bankruptcy Assassin” scenario. Set the pirates as your friends, and keep a good relationship with the Splits (or any other race that doesn't already hate you).
• If you want to hunt the Guild, there's absolutely no need for a restart. Just wait a few game hours as the guild needs to build up strength to be a serious opponent. The Galactic Police pays well the destruction of any Pirate Guild ship. But beware, the Guild then may decide to target you and to break in your industrial and military sectors. Also notice that pirate ships are well equipped and sometimes overtuned, so capping them can be rewarding.
• You have to understand that this plugin won't change everything in the universe the second it's enabled. It can take up to several hours before the bases can buy enough ships and defenses to become a real threat. But you can be sure that they will. So, if the Guild doesn't like you, you'd better be prepared. :)
• Try to get a Jumpdrive as soon as possible. Without it, you'll always arrive too late during invasions and attacks as most of the guild members are equipped. You can find one on some legit ships, but if you manage to capture one, you should play the lottery instead (less than 5% of ships have a jumpdrive in the vanilla game). You can buy one at the Goner Temple (or from the Terracorp station, iirc) if your standing is good enough. Or, if Yaki Armada is installed, you can try to capture a Yaki ship (you'll find some of them patrolling around the universe), as they are all fitted with a jumpdrive.
• Understand that pirate ships aren't a simple annoyance anymore. They are now a real threat, especially against a young commercial empire. Do not hope to destroy a Pirate Base with a single M3 (or even M6) and a few missiles. You'll have to send a whole fleet to do the job. And you can expect a brutal counterstrike against your assets. So, don't whine because you've lost your new fully equipped TL or a few factories to the Pirate Guild, you've been warned ;)

There's a few game limitations and side effects of the Pirate Guild plugin you should be aware of.

• If you're not playing a new game from scratch with this plugin, and set pirates as your friends, you may still find some hostile pirate ships. There's no real way to prevent this. However all pirate ships are checked every 15 minutes, and correct relations are applied when needed. By the way, don't forget to apply your Friend/Foe settings to all your fleet from time to time to avoid friendly fire.
• There's a lot of differences between OOS (out of sector) and IS (in sector) situations. And “weird” things may happen when you're in the same sector as pirate bases. As an example, when a Yaki Mobile Base (from the Yaki Armada plugin) comes to refuel at a pirate base it may sometimes be attacked by the pirates (even if the two factions aren't currently at war) for a random reason IS that won't happen OOS. It's not really possible to prevent this, there's too many random elements in the game. But, tbh, it's more a feature than a bug :)
• Notice (and this is a general game note) that the sector you're in evolves much slowly than the others. So if you want the Guild HQ to grow fast, you shouldn't stay in the same sector.
• Sometimes hostile pirates will turn back red on you even if you give them a tribute to go away. Here again, it's a game engine limitation. It doesn't happen very often. And finally it's like in real life :)
• It can take some time to retrieve the Pirate Guild's Top10 pilot list. So, don't think that the game is crashing when you're asking for it to any PB. Just wait a few seconds, and you'll get it.
• Do not press [ESC] to quit a communication screen, always use the 'bye / logoff / cancel' button.