This page of the guide to GreedFall has the walkthrough for The Prince's Secret, one of the main quests.
Talk to Admiral Cabral about the ruins. You receive an order to ask Petrus about the problems of Nauts from Theleme. You can do this in direct conversation with your companion, or in a camp. Then, go to a meeting with Bishop Domitius in San Matheus. After that, talk to the Nauts at the docks.
Go to the specified location and start eavesdropping on soldiers. Go to the barracks and to the prison - bribe the guard (80 gold, don't fight with him because you will lose reputation) to get the cell key. Release the Naut and then go talk to Bishop Domitius.
You need to search the Naut warehouse again - jump over the fence and start sneaking. If you don't want to do that, fight your way through the Naut - this will cost you a few reputation points.
Find the evidence from the port administrator and then go further towards the hangar. You need to sneak or fight with the Naut (which will further reduce the reputation). You will find boxes and more notes.
Time to gather evidence against Ordo Luminis... Go to his house, defeat the guards inside and find the letter from the Inquisitor. Tell everything to Mother Cardinal and you will get +1 Theleme reputation point.
Go back to Admiral Cabral and tell her all about everything. Go to Constantin and tell him about the betrayal - this will finish the quest. You will get 1,400 XP, + 1 Naut reputation point and start Dangerous Bets side quest. You will automatically start another main quest - Treason!