Desyncronization in Assassin's Creed III is like failing a mission
What causes Desynchronization
If your character dies, Desynchronization will occur
You can die from combat damage or falling from too high
Attacking innocent people
Attacking allies, civilians, farm animals, and more, can cause Desynchronization to happen.
If you do this by mistake once or twice, you might get a warning but it wont create Desynchronization. But if you go on a killing spree, you will get Desynchronized.
Moving out of bounds
If you move out of the mission area or too far from an NPC you are supposed to escort, you will get the warning message:
You should immediately comply by moving back to the zone you are supposed to be in for that mission.
Failing an objective
If you fail a main objective, Desynchronization occurs.
Note that failing optional objective does not lead to Desynchronization, however it prevents you from achieving full Synchronization Rate
Losing your target
If you get too far from a target you are chasing, you will get the message:
If you don't catch up, you get desynchronized.
Using wrong weapon
For example using lethal weapon where mission called for non-lethal. You will get a warning such as:
and then get the message:
What happens if you get Desynchronization
If you trigger the Desynchronization, you respawn back at the last checkpoint.