The Rogue Faction is positive-only, meaning it's impossible to lose reputation depending on your actions. You can acquire Rogue Reputation by completing Missions and events, or purchasing the corresponding packs in the  Outlaw Faction Store.

The Rogue Faction store is where you can acquire Uncommon- Rare Uranium, Outlaw Research Unlocks, Outlaw Warp Tokens, Outlaw Recruit Chests, Outlaw Research Credits, and Eclipse Armada Directives. This is also where you can redeem your Stella Hull Scan that is received from scrapping your Stella so that you can receive the Blueprints to rebuild it.

The currency used for the Rogue store is Eclipse Security Codes which is received from killing Eclipse Hostiles, and Eclipse Armada Loot received from destroying Eclipse Armadas.

The Stella is the most effective ship for both Eclipse Hostiles and Eclipse Armadas. By periodically scrapping your Stella, you receive Stella Particles (as well as the Hull Scan) which are used in the Outlaw Research Tree to increase Stella's power and abilities.

Important note, the Rogue store is run by Outlaws and as your Reputation increases, the items become more expensive.