Mission 7: Suffer With Me
Near the end of the mission, you will escort Noriega to the drop off spot where Mason will be told by Hudson to trust him. Immediately afterwards, you will take Noriega to a rooftop where he will tell you that Menendez is down below with a bag over his head and you are free to take him out. As we know, it isn’t Menendez, but rather Mason with the bag over his head. When he walks out, if you resisted killing Kravchenko, you will hear his voice repeating that Raul has people in the CIA.
This choice doesn’t affect the story per se, but rather the ending sequence of the game instead. If you shoot Mason in the head, you will kill him-- and if you capture Menendez at the end of the game, David Mason will retire. If you shoot Mason in the chest however, he will live, and show up in the ending with David and Woods.
Mission 8: Achilles' Veil
The main decision through this mission, as you first play as informant Farid, will be whether or not you kill Harper who gets captured when Raul shoots down his jet. The choice may seem inconsequential at first—well, except to Harper—but it actually has a ripple effect that can drastically change the ending of the game. If you decide to let Harper live, Farid will die and therefore he will not be present on the USS Obama when Menendez attacks it. Not a big deal right?
Except that when either Salazar or DeFalco, (depending on if you killed Defalco previously) shoot up the bridge, they will kill Chloe. If Farid is alive, he will jump in front of the bullet saving her. If he isn’t there, Chloe will die and she won’t be able to put a stop to the virus at the end of the game.
Other changes that occur if Harper is still alive are that he will shoot Salazar when he surrenders in the hanger, and he will be present alongside you for the next few missions and at the end when you face Menendez. As you can see, for the greater good of the world and the ending, Harper has to die; burned up face or not.
Mission 9: Odysseus
This is where the outcome of the major decisions start to come into play. The Obama is getting attacked by Raul’s PMCs and all hell is breaking loose. If you have successfully completed all the Strike Force Missions that were available, then you will be given a scene where Briggs is told that the China will do what it can to protect the Obama.
As mentioned in the previous mission choices, if Harper is alive, and you saved Chloe, then Chloe will die on the bridge by Salazar shooting her. If you saved Chloe during the Second Chance Strike Force Mission, then DeFalco will still be alive and will slice her throat. However if Farid is still alive, he will save Chloe from both Salazar and DeFalco, but will end up dying either way (shot by Salazar or shot by Defalco while simultaneously killing DeFalco.)
The next choice is immediately after and you will have the choice of shooting Briggs in the leg or head, effectively just wounding him or killing him. If you wound him, he will still be able to reactivate the Obama’s defenses that he shut down, which allowed Raul to access the bridge, to help fend off the incoming drones. If you kill him however, even if you are friends with China and their reinforcements arrive, the Obama will be lost. If you don’t decide to shoot Briggs in the head or body, then Salazar will knock him out, but he’ll still live and be able to activate the defenses.