--- I beat the game on the hardest difficulty and didn’t try to get the secondary objectives, then I went back and used “Quick Mission” mode to go through all the missions again on the easiest difficulty. It took a couple hours, but was well worth it. If you try to get all the secondary objectives while playing on the hardest difficulty, you’ll have a much harder time with it.

FAQ-

"Do I have to finish the whole mission to get credit for the secondary objective?"

--- No, you don't have to play the missions all the way through, as soon as you get the secondary objective, you can quit and it will still give credit for it! (Props to XX NUKEMAN XX for figuring this out!)

"How do I tell if I completed the secondary objectives for the mission?"

--- If you go into "Quick Mission" mode, when you highlight a mission, it will give you a description of the mission, at the end of the paragraph it says "Secondary objective completed" if you already completed it. (This is the way to tell which ones you need to go back and get)

Mission Names:
1. “Need your cojones, son” - Neutralize fleeing vehicle
2. “Knock’em Dead” - Neutralize fleeing vehicle
3. “Unpleasant Surprise” - AUTOMATIC
4. “This place is an inferno” - Neutralize fleeing vehicle
5. “You’ll be inserted solo” - Neutralize fleeing vehicle
6. “The price of peace” - Neutralize fleeing vehicles
7. “On your own” - AUTOMATIC
8. “Failure is NOT an option” - AUTOMATIC
9. “Get me Rosen” - AUTOMATIC
10. “Who the hell are these guys?” - Neutralize fleeing vehicles
11. “Codenamed Farallon” - Neutralize fleeing vehicles
12. “Just shut up and do your job” - AUTOMATIC

1. “Need your cojones, son”

After you destroy the two artillery tanks, you’ll head up through a cave-like pathway to secure and hold the bridge. As you exit out from the cave-like pathway, you’ll see the bridge up ahead. The enemy vehicle will sit there for a bit and then head down off the bridge to your right. The easiest way to take this vehicle out is to assign your team to destroy it. Right as you exit the cave/path, run up and take over on the closest rectangular box, pull up your 3D map and assign your team to attack the fleeing vehicle, within a few seconds it will be destroyed. (It helps a bit if you shoot at it as well)

2. “Knock’em Dead”

After you reach the rally point at the camp entrance, you’ll need to continue up the path you’re on until you’re overlooking a valley/construction area with lots of enemies spread out in the middle. The fleeing vehicle will be parked down to your left. The easiest way to take this out is to sneak up on it and kill the driver. Simply run down the pathway that leads down to the valley, and stay along the leftmost wall. (None of the enemies will notice your location if you stay to the left along the mountain wall.) As SOON as you have a visual of the driver, shoot him in the head. (A sniper or single shot will guarantee accuracy, and no chance for vehicle to escape) Once you kill him, the secondary objective is complete, even though later you’ll still see a purple rally point on the vehicle, as long as you kill the driver, you’ve neutralized the fleeing vehicle.

WARNING: Once you open fire on the driver, you will alert all the other enemies in the area, so immediately continue forward to the fleeing vehicle and take cover to the left of the huge crane, by the dirt pile. Then continue around the left of the pile passed the vehicle and cover on the pile to the passed the vehicle, this will give you a MUCH better shot on the enemy hostiles.

3. “Unpleasant Surprise”

After this gunride mission, you will automatically get credit for completing the secondary objective.

4. “This place is an inferno”

Once you reach the mule and equip yourself with a Zeus T2, head to the next rally point, (the location of tank.) As you approach the area where your ghost friendly tank is taking enemy tank fire, you’ll see metal roof access, DO NOT take them, however peak left around the corner of the building, directly at the bottom of the metal stairs. You’ll see a your target, the tank, and also a gunner vehicle just to the left of the tank. First shoot one rocket at the gunner vehicle, fleeing vehicle neutralized. Then several rockets to the tank will finish it off.

TIP: Just peak around the corner, shoot, and then cover, reload; you do not need to keep your reticle/aim locked onto target after you shot the rocket, since the targets are not moving.

5.“You’ll be inserted solo”

(There are two parts to this secondary objectives)

PART 1: Once you reach the cemetery entrance you'll be ordered to take down the re-enforcements before you can move on. At about the time you get the orders you should be around a street corner, and to your right should be two arched piles of sandbags, behind them to the left is a building with metal roof access stairs. Go up these stairs and cover on the wall at the top of the stairs, facing the direction you just came. A support troop truck will start to come down the street at the top of the hill, as soon as you see it scope in and kill the driver. Then a second support truck will come from the right at the bottom of the hill, and drive towards the sandbags, scope in and shoot out this driver as well.

WARNING: The second truck is quick, so if it passes by, just kill yourself and you'll load the last checkpoint.

PART 2:This one is harder to explain, so I made a map to reference to. After you are told to take out the snipers with a counter-snipe, go to the MULE and grab a sniper, and to make things easier, grab a sub-machine gun for secondary. Once you do this, follow this map.

 

(some people can't see the image, so click the URL below)
http://www.kickassclanwars.com/images/content/5mapar7.jpg

MAP LEGEND:
Blue Line – Path to take
Red Target’s - Enemies along the way
Yellow Line - Path of fleeing vehicle
Green Arrow - Shot through windshield to driver
Red Shaded Oval - General area of hostile ground troops

Once you grab your sniper, turn around and head out behind the MULE, make a left and move towards an archway and stop at point #1. Through that archway at the opposite end of the courtyard will be two hostiles, one on the rooftop and another directly below him, take them both out from point #1 location. Move into this courtyard area and look for stairs along the immediate left wall, go up them and take a left and go up another set of stairs. Take this rooftop all the way to the end and down another set of stairs onto the street. Head along that street and stop at point #2. At this corner there will be a hostile on the roof in front of you, slightly to your left. Once you kill him, cover on the wall and wait for the support vehicle. (The vehicle will only come once you open fire) It will pull in and stop at the T mark at the end of the yellow line, once it stops take your shot into the vehicle cabin and eliminate the driver; secondary objective complete. Finish off the rest of the hostile group troops with your sub-machine gun and proceed to rally point.

6. “The price of peace”

When you’re moving to be extracted by the Blackhawk 5, you’re moving towards the extraction rally point. As soon as you reach this rally point he’ll tell you to hurry up, and say he is taking fire, then he will immediately announce he has been hit and is going down. Once you trigger this situation by running to the rally point, turn around and take cover on the skinny rectangular flowerpot box, just in front and to the left of the merry-go-round. You’ll have to anticipate two enemy helicopters dropping down to supply more hostile ground troops. When the first one touches down, it’ll be in front of you. Shoot out the gunner on the side of the helicopter, then the second one will touch down to your right, in front of the fountain, shoot their gunner out as well, and secondary objective will be completed. AS SOON as you shoot out the second gunner, un-pin yourself from the flowerpot box and run back to the point where you were supposed to be extracted, and cover on the middle flowerpot box closest to the building. Take out more troops until your hummer picks you up. You HAVE to shoot a certain amount of enemies in order for your ride to come, you can’t just cover and wait it out.

WARNING: As you’re running back to cover by the building, beware of enemy troops that may be off to the left as you’re running back, sometimes they run behind you while you’re shooting the gunners.

TIP: If you miss the gunners and the choppers fly away, kill yourself or run out and die, and then start the checkpoint over. Once you gain awareness on everything that is going to take place, it should become fairly simple to complete.

Here is the run down on what you need to do.

1. Move to rally point for extraction to trigger the “Blackhawk 5 Down” situation.
2. Turn around and go to flower box front/left of merry-go-round and cover/wait for enemy helicopters.
3. Take out the left helicopter’s gunner
4. Take out the right helicopter’s gunner
--- Secondary objective complete.
5. Run back to middle flowerpot closest to building and cover, and shoot down troops until extraction comes.

7. “On your own”

When you start this mission you are waking up and there is a solider who tells you that you’ve been knocked out due to the blast. Once you stand up you’ll get a checkpoint, and secondary objective will be completed.

8. “Failure is NOT an option!”

You’ll automatically get credit for the secondary objective, as soon as you load into this mission.

9. “Get me Rosen”

You’ll automatically get credit for the secondary objective, as soon as you load into this mission.

10. “Who the hell are these guys?”

Once you're granted support from Abrams (shortly before you're granted support from Little Bird) run to your right and you'll see a building with a ramp up the side of it, head towards it and up there, once you see two purple squares (fleeing vehicles) on your HUD, pull up your 3D map and command Little Bird to attack and neutralize them, once she does so your secondary objective is completed. OR, you could just take them out yourself, or with a team mate. (Personally, I found it easier just commanding Littlebird to do it.)

11. “Codenamed Farallon”

After you move into the facility you’ll be ordered to secure two points in the area. Move to the left rally point and secure it by taking out all hostile threats, then hurry towards the other rally point. At about halfway to the other rally point you’ll be cut off by an enemy chopper. The chopper touches down and drops more troops. Try to cover on a flowerpot box and use single shot to kill the gunner on the chopper. Once you kill him, your secondary objective will be completed.

12. “Just shut up and do your job”

You’ll automatically get credit for the secondary objective, as soon as you load into this mission