Communication between the playership and the Yakis is done via the ECS library. Target a Yaki ship or mobile base at less than 8km of your ship and press the keyboard shortcut assigned to the ECS library to comm with it. Options and how the pilot will react according to your guild rank and your general reputation with the Yaki faction. The basics communication options allow you to ask a ship for the location of a mobile base, for an escort or to surrender. You'll also be able to help a pilot when he is attacked by the police or military forces. The ECS system is very important and is used for most missions of the guild.
Yaki ships and mobile base controlled by this plugin are (a bit) smarter than standard ships from the game. Each mobile base will use its fleet to attack race assets in the universe. When attacked, they will release drone and send defensive fighters, and if the base is too badly damaged or has not enough fighter left, the base will jump away in a more secure sector to regroup. They are also able to repair, rearm, and refuel at pirate bases. By the way, mobile bases are also able to use covert state to appear as a Paranid (or any other race) Factory Deployer or any other kind of 'legit' TL on the radar to move across a sector without being attacked by police forces. You can't communicate with a Yaki Mobile Base while it's under cover.