To complete Cartagena you must:

Navigate the Sewers
Rescue some Old Friends
Locate the Viceroy

You enter the city through a secret sewer entrance. After a quick talk with Anne and Rockfish you need to figure out the raft puzzle. The raft is actually an elevator, but it must be operated by someone other than the rider. Stand on the raft and ask either Anne or Rockfish to turn the LEFT wheel which drains the water and lowers the raft to the next level.

Exit through the door and when you hear Anne calling you, look up to your left to talk to them through the vent. Another set of Drain/Fill wheels are located in this room so you can fill and drain the previous room from here. Shut the door (very important) before you fill the room, then tell Rockfish and Anne to get on the raft. Then drain the water and bring them to your level.

Another raft awaits in a rapid flowing canal. A pair of doors needs to be opened before you can exit, so have Anne and Rockfish stand on either side then click on them to have them pull the chain and open each door. Cut the rope with your sword to free the raft and start down the canal. Anne and Rockfish will jump on for the ride.

Rockfish sinks like a rock leaving just you and Anne to finish the mission. Walk around and enter the door to find a large cage suspended over a pool of water. Inside are Jake and Elizabeth - apparently the Viceroy is holding them as bait to capture you. Freeing them is your next quest.

Walk to either end of the upper catwalk then go down the spiral stone stairs to the bottom level. More steps lead down to the torture chamber. Save your game before entering. As soon as you enter the guard will turn and disarm you with his whip. When combat begins you must DODGE his attacks by leaning towards the direction he his swing from. It takes a bit of practice but once you dodge his whip three or four times you will drive him back far enough that you can grab your sword from the wall.

You are unable to beat him in standard combat so swing at that big pot of molten metal to spill it out onto the floor. The guard will burn his feet and end up inside one of his own torture devices. You can explore the room to discover some grisley items of death and a key.

Take the key back to the previous room and upstairs to the upper catwalk and use it to unlock the door to the Viceroy's study. Inside are four suits of armor along the wall. Click on each to open the compartments on the shields and obtain the four symbols. Return to the lower walkway in the previous room to free your friends.

Each wall has a lever which is locked until you place the matching symbol in the recessed area. Then you can flip the lever down. When all four levers are down you can then go flip the lever in the center of the room to extend four bridge extensions and lower the cage, thus freeing your brother and Elizabeth. Head back upstairs to talk to them.

After a brief conversation with your friends you can go back into the study and click on the bookshelves to the right of the suits of armor. Inside is a secret room with jars containing all the left arms of all the dead Brethern. Seems somebody is keeping a sick collection and that person has just walked in behind you.

It turns out that the Viceroy is Marquez, RedJack's old and once-trusted companion. Apparently he faked his death 17 years ago and has been up to no good ever since. He walks in with the severed arm of Rockfish and starts an almost friendly chat with you. It doesn't take long for him to get down to business. No matter what you do or say you will end up in the belly of one of his ships as he sets sail for the final reunion at RedJack Island.