In order to get the Liberator of Rubicon ending — and the Liberator of Rubicon Trophy along with it — you must choose to play the following Missions when forced to make a Decision:
Prevent Corporate Salvage of New Tech (Chapter 3)
Destroy the Special Forces Craft (Chapter 3)
Ambush the Vespers (Chapter 4)
Eliminate "Cinder" Carla (Chapter 5)
This makes Bring Down the Xylem your final Mission of the playthrough, and completing it gets you the Liberator of Rubicon ending and the associated Trophy. If you're going for this ending on a New Game+ playthrough, there's one extra step:
During Attack the Dam Complex, choose the "Refuse" option when given the choice