This is a highly missable trophy with several requirements, some of them non-obvious. As I learned first-hand, failure to meet any of the requirements will require a previously loaded save or a new play through.
1. For the side-quest, "The Origins of Theleme", you must convince the Mother Cardinal to reveal the truth about San Matheus. This can be accomplished by exposing Brother Virgil and completing the remaining objectives. I recommend bringing Petreus and making a backup save prior to turning final step of the quest in to the Mother Cardinal. Any conversation choice mistakes will cause the Mother Cardinal to keep the secret of San Matheus. Reload a previous save if necessary.
2. For the side-quest, "In the Name of Science", you must not kill Doctor Asili. Instead, gather enough evidence to convict him at trial and watch his execution.
3. You must complete all the companion quests for all the companions and their relationship status must be at Friendly (or Loving). This includes Kurt; he cannot be a part of the coup, so complete his quests as early as possible.
4. When choosing the High King, give the crown to Dunncas.
5. You must be at Friendly status with all 5 of the factions prior to recruiting their efforts to stop Constantine.
6. At the final stage, kill Constantine.