See Operation True Heirs for more info.
No matter what you do, or what choices you make, this achievement will always unlock upon finishing the final mission "Infiltrate Alpha Protocol". One thing your choices will decide however, is who you fight against for the final boss fight. One boss will man a nearby mini-gun, while another will use an infinite amount of RPG's to take you down.
For the boss with the mini-gun, do not move! Wait for other enemies to come for you, and take them out first. Once you do, just wait for a pause in his shooting, and then follow up with Chain Shot. If you've put a lot of points into the Pistol tree, you should be able to pull off a critical hit off while blind-firing behind cover. If so, use a critical shot or two to drop his endurance, and follow-up with a Chain Shot.
For the rocket touting boss, you'll have a lot more opportunities to damage him, but at a cost. He has the ability to destroy cover with his rockets, so you'll always need to be on the move. That means you'll need to drop his henchmen first before you start on him. Of course the usual Chain Shot strategy works beautifully here, so stick with it, and you'll drop him no problem.