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:
Tatooine
Thorazan Outpost, Sea of Dunes
Alderande
Circle of Commerce, Col du Roi
Quesh
Republic mining camp
Hoth
Zerek Outpost, Space Graveyard
Belsavis
Watchtower of the Republic, High security sector
Voss
Kri-Ta outpost, outskirts of Pelath-Ri
Corellia
North tram station, Government district
Ilum
Republic Base Camp, Western Ice Layer