First off, is the one they are hunting the player?
Tonal cities seemed to have been friendlier to AI pathfinding then some of the other islands so conducting searches would not be all that difficult but you would still need to test which areas of the city would be friendlier than the rest. I would recommend having vehicle patrols on the main roads and large groups around the intersections while individual units randomly searched the back alleys and merchant yards. I'm really unsure of how your story dumps the player (I assume) in the city but if you do not want the player killed, you will most certainly have to setcaptive him. You could also use the invisible targets and setpos them near the player when he is detected to increase the fear factor and also represent the poor aim of the persuing units. I think immersion would best suit this mission and if you really want the player to feel trapped, you would not need to search for him. Sounds can be implemented to create panic and the feeling of being closed in on. Place units on rooftops, courtyard entrances and such while groups and vehicles patrol dangerosuly nearby. Place the heal point in the middle of the city and have the player strategize on how to escape without being seen. Place a trigger which encompasses the city and set it to detect when the player is no longer present. That way the player can take his time to escape, thinking he is succeeding in evading the patrols while tension of nearby alleyways erupt in sounds of searches and occasional gunfire and screams that may force the player to return to the dark corner of a nearby shack and wait for the comotion to die down or move away. Then when the player reaches the trigger, just insert a cutscene showing the player in his exact location while you setposition enemy nearby and have them close in on him and arrest him. you could then return control to the player remove his weapon if he had one and order him to mount a vehicle for transport to the interrogation camp. If he tries to flee, setcaptive him to false and actually give him the chance to flee with them on his tail. Otherwise, he is yours for the control.
But you should also consider the backfire...Don't depend on the soldiers in the city to be used in the cutscene. If the player is good and takes his time, he could eliminate all of the units in the city at his leisure. Even if he has no weapon, luck could have one of the ai to fall from a building or one get run over by a patrolling vehicle and provide the player with a firearm. So, with that said...have your intercept crew used in the trigger out of harms way, and then setpos them within 50 meters of the player out of cameras view while they close in on him. ALso don't fail to place the trigger at a point where the intercept crew doesn't end up battling ai paths in alleys or rocks or whatever.