With the Conquest mode, new NPCs appeared, on certain planets, in outposts of each faction.
Each location can have either a Commander (5 million HP or a Veteran Battlemaster (800K HP). They are located in enemy outposts, so you will be tagged PvP.
Once defeated, each party member receives a "Flagship Blueprint: Encoding", and the Commander also has a chance to drop a "Flagship Blueprint", used to unlock coins in the ship (maximum 12 blueprints per. Commanding officer).
Commanders respawn after 3 hours, but have a shield on them making them immune to damage (not Battlemasters), which lasts 6 hours or when the guild that controls the planet has bombed them, disabling their shield. This bombardment, named "Flagship: Galactic Hunter Parade", can be purchased from the fleet, from the Planetary Conquest Gear NPC, for 1 Dark Project.
Here is the list of Commanders with their locations:
Thorazan Outpost, Sea of Dunes
Circle of Commerce, Col du Roi
Republic mining camp
Zerek Outpost, Space Graveyard
Watchtower of the Republic, High security sector
Kri-Ta outpost, outskirts of Pelath-Ri
North tram station, Government district
Republic Base Camp, Western Ice Layer