The Janissaries
After talking to the merchant, head to the area marked on the map. If you enter Eagle Vision, you'll be able to follow a trail right to him. Follow him through the crowds by blending in. Try not to get too close or to far and just follow him. When he goes outside, stay indoors. After cutscene, he'll come back inside but not after breaking up the crowd outside. He'll do it again inside but it will be easier to stay concealed. Follow him this second time until he meets another Byzantine. They will stay behind while he goes ahead. They will be looking for you.
Instead of going past them outside, just keep going straight ahead and then take a right to circumvent them and you'll be right back on his trail again. I am not sure if this part is scripted but as you follow him, watch out for an enemy trying to stab you in the back. You'll hear a gasp from the crowd and you will only be given a split second to hit the strike button. If you fail, you'll take massive damage but if you succeed, you'll reverse the attack and kill him.
After this point, you will have to get by groups of guards in front of doors. You should use a bomb to distract them since it's the bonus objective but you can also use your assassins to get rid of them or you could just go around them all together. Climb up on a roof where they can't see you and just continue your pursuit. Eventually you'll have tailed him far enough and the mission will end.
The Arsenal Gates
Walk around the area and bribe the three heralds marked on the map. After that, a riot will start. The rioters will be attacked and you have to defend them. Watch for the markers indicating soldiers. When they enter the crowd, come up behind them and kill them with your hidden blade. As long as they don't target you, you can go on killing them like this until they are gone. Just be careful to be quick about it because you need the rioters to survive.
Arsenal Infiltration
With all the chaos in the area, activate Eagle Vision and follow the trail to Manuel. If you are lucky, you can run all the way there but you may also get attacked by enemies. You can still just try and out run them if you want. You will follow the trail all the way to the docks until it goes into a building. Go into the building, watch a cutscene and then you need to flee the area. Basically just run all the way back from where you came.
For the bonus objective, you need to assassinate someone from a zipline. If you find the opportunity to do so during the mission, do it. If not, on the way out you will find some boats that are half finished. If you climb one of them, it will have a zipline and there is a guard patrol just under it. The mission finishes when you get out of the area.
Portrait of a Lady
Head towards the Bazaar and activate Eagle vision. You are looking for a man sitting on the floor with a couple of other gentlement. Scan the crowd until you find him. When you have found him, unleash your fists of fury. Keep hitting him until he tells you where the portrait is.
Head towards the merchants location. If you happen to have a money bomb then this will provide the perfect distraction for grabbing the portrait. Any other solution you can come up with will work too. Once you have the portrait, head out of the bazaar and return it to Sofia.
Signs and Symbols, Part 2
Head over to the mission start point and stand on the ledge looking NE. The symbol you are looking for (in Eagle Vision) is the one under the broken section of Aquaduct. Jump down and collect it. It's best to climb the building next to that spot to collect it.
The Forum of the Ox
Go down to where the gun powder is and turn left. Go all the way to the left and you'll find a cave that leads through the wall. Once you come through on the other side, you get into a race with the boat. Make sure you keep moving. At any given point, it should be pretty obvious what you are supposed to do next. Don't stop moving or you may get shot, though, and lose your bonus objective.
Just a few things to keep in mind. Any time you see a swinging hook, make sure you turn it into a long jump. When you start to see fire, just run through it. When you finally catch up to the boat and you are ziplining over it, you have to assassinate the guards on the boat. And after the boat crashes, you'll get into a four on one fight but they are all just simple guards. Counter one and you can just chain it and kill the all with one button press each. Be careful at this part though because you don't want to go and lose health here.
Loot the chests and investigate the middle secret door section. Open it and claim your key.
A New Regime
Walk with Maria to meet with Abbas. After everything goes to hell, you need to escape Masyaf. Head back into the library and instead of going downstairs, go upstairs and through the big window. Keep running down the hill to escape Masyaf.
You will bump into your son here. Instead of running, you will have to now fight your way out of the city. Use throwing daggers to kill any enemy that is preparing to assassinate you. Usually the camera will shift in some way to show you these enemies. Try to stay by your son's side while you are fighting, if you get too far, you will desynchronize. Some fights will serve only to slow you down but some fights you will have to finish. These are usually the fights that are listed as target in the upper left hand corner of the screen.
Keep fighting your way down the hill and you will be ambushed and have to head back up the hill in a different direction. You will then have to leap down. Be warned that I experienced a glitch here where Altair's son got stuck going up the hill, I don't know how it happened but dying seemed to fix it. Exit Masyaf to finish the memory.
