G.I. Joe: Operation Blackout

Each mission, except for the three vehicle ones, has a secondary objective for you to complete. As you're playing they will appear in a blue box underneath the main objective in the top right corner of your screen. They only show up when you reach a point in the mission where you can start working on them. You can also see what the secondary objective was at the end results screen of each mission but other than that you can not see them elsewhere in the game. The mission selection screen does track the ones you've done along with collectibles.

Mission 1- Capture the Flagg: Use the last AA turret to destroy the remaining skystrikers
The third AA turret is just after the first encounter with the boss, on the left side of the ship again. This is before you follow the stairs down inside.

Mission 2- Lights Out: Destroy all Cobra machinery
In the final area of the mission, around the refinery, there will be four large oil drills. They will be highlighted red. Shoot or melee them a few times. One is down a secluded path to the side of the area.

Mission 4- Cold Case: Defeat Zartan during the comm station encounter
When you get to the second comm station Zartan will attack you. He stays up high to snipe you and teleports each time you attack him. You can fight him without having to engage any other enemies.

Mission 5- Scarcity of Freedom: Secure all Cobra data caches
These are computer terminals that you have to interact with. The first one is right in front of you after Mainframe opens a door for you. There's three more throughout the level. They're highlighted red again.

Mission 6- Come With Me If You Want to Live: Disable all flight control towers
There's only two of them. They're at the end of the mission between the two hangars you have to check for a Rattler. You're looking for big red rectangles (power banks, I guess?). Destroying those disables the towers.

Mission 8- It's a Trap!: Destroy all B.A.T.S. pods
These look like big teleporters that enemies spawn out of. You have to destroy three of them at the start of the mission as a main objective. After that, there are seven more in the level that count for the secondary objective. The first two are in the room you first fight the boss in. Another two in the red lit room where you fight the boss a second time (one on the catwalk opposite of the one you entered on and one underneath the central platform). The final three are in the small room where you fight the boss for the third and final time.

Mission 9- Made in Japan: Steal all scrolls
Three scrolls. They're all after the long drop off the cliff and before the second charge.

Mission 10- Fury & Silence: Light all of the incense
Four incense to light. The last one is actually beyond the point you trigger the final fight with the boss. Make sure to light it before defeating him.

Mission 11- Nothing Personal: Destroy all statues of Cobra Commander
There's six red highlighted statues to destroy. They are all inside at the area where you have to survive in the blue ring during the hacking process.

Mission 12- First Light: Destroy all Cobra Rattlers in the hangar
Not far into the mission you will have a battle inside a large hangar. There will be four airplanes/jets highlighted red for you to destroy. I would not recommend melee-ing these. I did and got glitched inside of it.

Mission 13- Unplugged: Defeat Lady Jaye and Defeat Scarlett
Technically two secondary objectives here but they're done in the same area. At the end of the mission you will have to defend against three waves. Lady Jaye appears for the second wave and Scarlett appears for the third. Make sure you kill them before eliminating all the regular enemies or they will disappear. It has also been reported that it won't count if the turrets kill them so it is recommended not to activate any. Make sure to play as Baroness when you do this for another achievement!

Mission 14- Undo What They Did to USS: Use the last AA turret to destroy the remaining Cobra Rattlers
Basically the same as the first mission. The third AA turret will be in front of you after crossing the bridge.

Mission 16- Enemy of my Enemy: Obtain all Cobra intel caches
Similar to Mission 5, these are computer terminals again. There are four of them all inside the building where you have to "destroy the fortress's consoles." Make sure you get them before you exit outside.

Mission 17- Freedom Squad: Defeat Zartan
At the beginning of the mission when you're assaulting the throne room with the tank, Zartan will appear on the upper level of the circular room. He'll teleport as you attack him and you'll have to deal with some regular enemies this time as well.

The achievement will unlock when you finish the mission, not as soon as you complete your final objective.