With the Conquest mode, new NPCs appeared, on certain planets, in outposts of each faction.
Each slot can have either a Commander (3500K HP or a Veteran Battlemaster (571K 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.
Commanders respawn after 3 hours, but have a shield on them making them immune to damage, which lasts for 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
Zaroshe Outpost, The Sea of Dunes
Alderande
Talarn Outpost, Juran Mountains
Quesh
Imperial Garrison
Hoth
Frozen Wake Outpost (Gelvif), Space Graveyard
Belsavis
Imperial Command Post, High Security Sector
Voss
Overseer's Outpost, The Outskirts of Pelath-Ri
Corellia
Business sector, Government district
Ilum