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:
Zaroshe Outpost, The Sea of Dunes
Talarn Outpost, Juran Mountains
Frozen Wake Outpost (Gelvif), Space Graveyard
Imperial Command Post, High Security Sector
Overseer's Outpost, The Outskirts of Pelath-Ri
Business sector, Government district