Phase 17. Closer and closer
Autopsy is in phase 6 of Q2.49 Anatomy of a Crime...
If you are convinced that Ramsmeat is the culprit, you'll be moved to phase 25.
Phase 18. Azar Javed
If during the autopsy you guessed that Azar is impersonating Raymond (and if you're unsure of that, check out the crypt in the cemetery), pay a visit to false Raymond (M8.2).
Phase 19. Subterfuge
Tell Raymond-Azar that you weren't able to make any sense of the autopsy.
Phase 20. A Trap
Go to Raymond once more, listen to details of his plan and tell him that you'll take care of Ramsmeat by yourself (M8.24, M8.37).
Phase 21. The Tower
You don't have to harm Ramsmeat, but it's a good idea to tell him about Javed, if you haven't done that already. Tell Raymond that Ramsmeat is dead. In the next conversation, about a tower in the swamp, you'll get Keth'aar Sephirah.
You can catch Raymond-Javed and expose him at once - in this case he'll kill you instantly and there's nothing you can do about it...
Phase 22. Fake no more
Now perform the quest Q2.58. Monoliths and enter the tower (M10.19).
Phase 23. The Secret within
Inside the tower, in a chest, there's a book that Azar wants.
Phase 24. Azar's escape
When you leave the tower you'll finally come to face Azar - take some time inside to prepare for battle. Azar will first summon an Ifrit, a fiery beast that you'll have to kill. Later, Azar and Professor fill face you together. Strike them hard enough and they will paralyze you and run away.
When you lay unconscious by the tower, a battle between the Order and the Scoia'tael will take place. Chapter II comes to an end.
Phase 25. Autopsy results
So, you think that Ramsmeat is the culprit?
Phase 26. Ramsmeat Contract
When you go to Raymond's (M8.2) you'll get a quest to kill Ramsmeat.
Phase 27. Ramsmeat dead
Battle with Ramsmeat (M8.37) won't be easy, as 10 of his men will come at you the moment you threaten him (use steel sword, group style and swallow a Swallow). By his body you'll find 900 orens and yellow meteorite.
Phase 28. The Tower
Tell Raymond that you've killed Ramsmeat - you'll get Keth'aar Sephirah and arrange a meeting with him...
Phase 29. Opening the Tower
You now have to complete Q2.58 Monoliths to get inside the tower (M10.19).
Phase 30. Tower's Secret
Inside the tower you'll find a chest and inside it - a book. Take it with you.
Phase 31. The truth
When you go outside, Azar Javed will expose himself before you and take the book that you found. The remaining part of the quest is the same as in phase 24.
Q2.28. The Crown Witness
Phase 1. Prisoner
Quest begins when you talk to Raymond (M8.2) in phase 3 of Q2.27. Vizima Confidential.
Phase 2. Captain
If you ask Vincent about the prisoner, he won't tell you anything.
Phase 3. The Bribe
Jethro (M8.23) can give you some information, but you have to bring him a unit of Fisstech. You might have some of it that you've collected from bodies in phase 4 of Q2.27. Vizima Confidential. You can also buy it from Coleman (M8.24).
Phase 4. New source
If Coleman is dead...
Phase 5. Salamanders
... then you might have to find Fisstech by some bandits' bodies - you'll find bandits mostly in the nonhuman district (M8.6).
Phase 6. Fisstech for Jethro
Give the drug to Jethro (if he doesn't want to talk to you, leave the dungeon and enter it again).
Phase 7. Prisoner in the Hospital
Jethro will tell you that the imprisoned Salamander is in the hospital.
Phase 8. The Hospital Raid
To enter the hospital (M8.30), you have to either bribe the guard or show him the city guard signet ring. You'll get it from Vincent Meis at the end of Q2.26. Suspect: Vincent Meis. Go the at night and bribe one of the guards that look after the prisoner. After the prisoner whispers Kalkstein's and Ramsmeat's name, 5 thugs will attack you. Kill them. A short conversation with the Prisoner will advance the quest Q2.27. Vizima Confidential and initiate Q2.38. Suspect: Ramsmeat and Q2.39.Suspect: Kalkstein.
Phase 9. The Interrogation
Conversation with Raymond (M8.2) sums up the investigation to this point - main leads point you towards Kalkstein and Ramsmeat. When after the hospital raid you talk to Shani, she won't be happy about your dealings, and tell you that the prisoner has been taken to "a safe place".