I have completed every assassination to this point. freed all the civilians, have talked to the person in the borrow. But yet i have been able to find/complete and of the missions before the assassination. I am in the correct city but it is dead. Any thoughts on what is wrong?

Explain to us exactly what was the last assassination you completed.

Are you in Masyaf?
If not, then don't continue, if so, then read on:

************HERE BE SPOILARS!*****************
The city should be empty, just make your way to where AlMuallim usually is.
************HERE ENDS SPOILARS!***************

If you aren't at that point in the game (although your description of the surroundings seems like it), then you might need to explain your problem a little more...

it said i had to go to Jerusalem. The last person i killed was William of Montferrat. I apologize if it isn't the last assassination i was not 100% sure.

Ah!
Don't worry! It is the last assassination.

I thought you meant after the last assassination!
Silly me!

I believe you have to go to the assassin's bureau.
And if you have already done so, then look at your map.
There should be a "clouded region", or a "fogged up" third of the map.
You can now enter that area. You have to climb one of the viewpoints.

And if you have already done that, and all the investigation missions, then you should have to go to the graveyard.
It should be marked on your map if you have completed all the tasks... >_>

I have been up all the view points. There still is Cloudy area, But i have yet to find the investigations. But all the civilians are freed.

Have you been to the top of the viewpoints in the cloudy area?
It shouldn't be "cloudy" otherwise...

Once you climb up one of the viewpoints in the area, you should get all the investigation missions.

Alright, ill give that a shot. Thank you!!!

... I think I'm coming down with something...
I'm being... helpful! *sniffle*