Here is the walkthrough of the quest I've found on this site, so if you can't figured it out just look here, it's true some quest book entries are missed here.
Greetzz,
VanessaHudgensFan
A Worm in the Apple
This walkthrough assumes that you accept each job given to you – there are lots of options in the dialogues to reject the jobs - so before meeting people you should do a SAVE.
Sail to La Tortue, Tortuga – go to tavern – talk to Vassal Bethune – QB Update
Sail to Port Royale, Jamaica – on entering the part of town with the prison in it Vassel Bethune talks to you & walks away – follow him – Enter house – Talk to Mateus Santos.
Mateus Santos – makes you an offer - pay careful attention to what he says and the conditions he makes. ( BAD things will happen to you if you don’t follow the rules).
There are time limits - 3 months to do the job - you can take as long as you like to go back to Santos to collect the reward for the jobs he gives you
BUT each job you do will lower your reputation by one level ( if your reputation gets too bad, merchants / storekeepers will not talk to you or sell you goods e.g. Food, Rum etc.)
If you accept 1st job – QB Update - sail to Boca de Yuman, Hispaniola – talk to Ambroz Bricenos on beach – kill him – Yes / No - QB Update
Sail to Port Royale, Jamaica – go and talk to Mateus Santos - gives you reward – offers you next job – QB Update
Sail to Bridgetown, Barbados
Go to House of Geffrey Bampfylde (between shipyard and tavern)
On entering automatically walk up to Geffrey Bampfylde – he talks to you – Bucho talks to you - Kill Bucho - Geffrey Bampfylde talks to you. - Kill him - Yes / No – QB Update
Sail to Port Royale, Jamaica – go and talk to Mateus Santos - gives you reward – offers you next job – QB Update
Sail to Grand Turk, San Salvador – on Grand Turk jetty talk to self – search for Pepin Bertillion he is wandering around the Port Area - Talk to Pepin Bertillon – Kill him - Yes / No – QB Update
Sail to Port Royale, Jamaica – go and talk to Mateus Santos - gives you reward – offers you next job – QB Update
Sail to Sao Jorge, Concepcion - Go to House of Amerigo Vieira ( next to townhall )
On entering Automatically walk up to Amerigo Vieira – he talks to you - Kill him OR Hire him as officer – ( if you hire him Mateus Santos will not know ) OR let him go – QB Update
Sail to Port Royale, Jamaica – go and talk to Mateus Santos - gives you reward – offers you next job – QB Update
Sail to Pointe a Pitre, Guadeloupe - Go to Church
SAVE HERE
Talk to Vito Leone – long talk - Kill him – Yes / No - QB Update ( Try killing Vito Leone then go back to Mateus Santos and see what happens ) - LOL
Sail to Port Royale, Jamaica – go to House of Mateus Santos
Enter – Automatically walk to Mateus Santos - he talks to you & disappears - fight Bodyguards behind you.
Go into study - Kill Mateus Santos – given items - Check your items & Quest Items ( F2 ) should have - Santos’ Ring, - Keys & 2 Books
Keys labelled - Study – Secret-ary – Alas Poor Yorick
Exit Study by Secret Passage – Talk to Camille Leone – Go through prison -fight more of Santos’ men – talk to Thomas the Terror – Go back to Camille Leone – Go to prison cell opposite skull on floor – Transported to Church - talk to Vito Leone – QB Update
Sail to Havana, Cuba
Go and talk to Vice-Admiral Benavides – gives you next mission – QB Update