The Prince’s Secret Walkthrough
This quest begins following the completion of the quest Mystery of the Ancient Ruins. Talk to the admiral, then head to San Matheus and talk to the bishop and general Fernando. Leave the general, turn to the left and see a fence. Behind the fence, you’ll see a soldier – it is difficult to bypass him. Ideally, you should have Nauts’ clothes. If you have them, you’ll be able to go past him and enter the port administration. Go upstairs, go through the barracks and find a note in the office.
Cross the fence from the port side and head to the warehouse. Search the first floor and the second floor until you reach a conclusion: there are no idols here, etc. Move to the port and question several people which are highlighted by ordinary markers. Go to the tavern and get to the inquisitor. Having talked to him, convince him to help by using Petrus (if he is with you) or charisma.
After this, enter the tavern, go down and get to the Coin Guard room through the brothel. The door is located under the stairs, below. Bribe the guard for 80 coins and use the key to open the cell and release the Nauts.
Go to Mother Cardinal palace and talk to her. You’ll get +1 to reputation with Theleme. Go back to the admiral in New Serene, talk to her and then to Constantin to complete the quest. At this point, you’ll learn that the cousin is infected by malichor.
Reward: 1600 experience points, +1 to reputation with Nauts.
Do you know why this quest would not trigger after completing “Mystery of the Ancient Ruins”?
It’s bugged. If you don’t talk to Constantin about the ruins before “Old Countries in a new world” mission this mission (THE PRINCE’S SECRET) will never trigger and will eventually make you stuck (since you can’t get the seal for the council meeting). They are supposedly working on it: https://forums.focus-home.com/topic/42016/can-t-get-seal-from-council-members-also-can-t-start-the-prince-s-secret-did-all-sidequests/8
Just to make the section of this quest where you have to get into the Naut hanger a little easier, put Vasco in your party, talk to the guard at the entrance and a dialog option for Vasco will be available. Choose this and Vasco will order the guards to let you in, that way you won’t need a disguise or have to sneak, risking a fight and a reputation loss. Hope this helps