You can only unlock the Alea lacta Est ending on your third playthrough (or New Game++), so get the Liberator of Rubicon and The Fires of Raven endings first and leave this one for last. To get this ending, make the following Decisions:
During Attack the Dam Complex in Chapter 1, choose the "Accept" prompt
Prevent Corporate Salvage of New Tech (Chapter 3)
Eliminate the Enforcement Squads (Chapter 3)
Coral Export Denial (Chapter 4)
Eliminate V.III (Chapter 4)
Making these Decisions unlocks the third and final ending: Alea lacta Est and its Trophy.