Far Cry 2

When ever you accept a faction mission (missions from A.P.R. and U.F.L.L. are faction missions) when you leave the building or on your way to leave the building you will get a phone call from one of your buddies saying they want you to go meet them. Once you go and meet them just keep pressing "Y" when looking at them, and then you will accept their mission. Now when looking at your map you will see a blue marker and a red marker. The Blue marker indicates where you must go to subvert the mission. The red marker indicates where you must go to just complete the mission. So basically all you need to do is always go to the blue marker's and do what your buddy asks you to do. If you complete the blue marker objective and there is still the red objective don't freak out, just go to red marker objective point and complete the mission. Just do this for all of the U.F.L.L. and A.P.R. faction missions in the Southern Territory to get this achievement.
NOTE: I beat the game and subverted all the missions, if this sounds complicated or hard, its not really.

Good Luck

Well, if you get to the "Heart of Darkness" place without this achievement being unlocked, then you have probably missed or accidentally switched from one of those "blue" (subverted) goals to the red (main) ones at some point.

BUT FEAR NOT. All completed subvert missions progress is stored anyway! So if you missed one then load some early save and replay (subvert) just that mission you've missed. You'll get achievement immediately.

UPDATE: If you didn't unlock the cheevo then you might have missed more than one. Keep doing those "subvert" type missions you could miss and you'll get the cheevo eventually. It's still better and faster than replay whole game.

Here's a little bit more detailed info: I finished the game and I've got all the cheevos except this one. Next I grabbed a game guide and started to look for what subverted mission could I fail or miss. To my luck, I found a mission where you need park the truck in garage and as I could remember I never did that mission. So, I loaded my 50% game progress save, replayed (subverted) ONLY that mission and voila -- the achievement popped.

Hope it will ease the pain for those of you who were going to replay whole game just to get this achievement. ;)

If you stuck with a faction in Act 1, you can go back in a new game and subvert those missions later. Just focus on this achievement as it's the harder of the two. Some of the subversions are difficult and require you to collect quest items. Just stick with them no matter what. If you don't get a phone call, don't panic. Just wait for a while and you'll get one. Then head over to the blue objective. Just keep heading towards the blue objectives and stay focused. The last few subversions are easier than the first few. If, at any time, you run out of syrettes, check guard outposts. They'll almost always contain a wall-kit. Other than that, just play it stable and keep it focused. You'll unlock this achievement at the end of the final faction mission after you give the fuse to Nasreen and watch the bridge explode, taking out the ship underneath it.

Structure: If you start with the UFLL, you'll end up switching to the APR after your first subversion. UFLL: 1; APR: 3. After subverting three missions for the APR, you'll return back to the UFLL. Simply subvert the last two easy missions and you'll unlock the achievement.

Additional notes:
1.) Sometimes the blue objective will be on the same location as the red one. In that case, just pause, note what the objective tells you and do that.
2.) There's a glitch in the second to last mission where Andre Hypollite will die no matter how many syrettes you give him. In this case, just follow Nasreen's instructions to complete the final faction mission.