Below you can find an description of completing the secondary missions, which you obtain from NPCs with exclamation mark over their heads. You can begin the mission after securing the particular region. During the dialogue, always choose the upper options to take the mission. They are divided on particular regions in which you can find the mission-givers. If any quest has any special requirements, you'll find it at the beginning of the description.
Yadong harbor 
Displaced residents: clean up the streets
In the northern west part of this map, on the marketplace you find Sanjay. Your mission is to conquer the rest of this region (Yadong harbor and Roadblock ).
When you do it, return to the marketplace and talk with Hasim. This conversation ends the mission and unlocks next ones in this region.
Displaced residents: make them suffer
To begin this mission, you have to complete clean up the streets. In the northern east part of marketplace you find Ehsan, who gives you another quest. You goal is to take over Khadwa . When you do it, return to Ehsan. You get few items in return.
The missing monks
The last one mission in this region you get from Siavash, who is in the northern part of a marketplace. He asks you to find three lost monks in Temple ruins .
When you get there, go to the destroyed temple on the southern east. You'll find corpses of monks. Return to Siavash and tell him about it.
Families torn apart: father should know
You get an access to this quest after finishing Families torn apart: tell them I'm fine..., which you get in Khadwan . Speak to Linh who is in the middle of a map. Your task is to inform her husband, Masoud, that their son Roshan, is lost.
Masoud can be found in Khadwan , in the center. Further part of this quest takes place in Monk village .
After the dialogue you get a key, with which you can open the door in the building. Take the key and pick up money and items from the room.
The big deal: dubious business partners
To unlock this quest, you have to finish The big deal: the missing son. Talk with Dilshad, who'll give you information about Nudda's travel to Sawmill .
In Sawmill  on the way on north, from the point on the southern west, you find a patrol with the suitcase required for this mission.
When you find a suitcase, return to the boy's mother on south of Coastal settlement . As a reward you get 42 000$.