This is it, the last mission. As soon as the mission starts, don't head out immediately. The last Rorke File can be found here as well.
Regroup with Hesh and follow him outside the train. Make sure to not lose your footing and fall from the train cars when jumping from each one. The place is constantly shaking because of the movement of the train, so it is easy to lose your targeting and balance. Continue forth until you encounter the first wave of enemies in this mission. Continue fighting through multiple enemies as you proceed onward. Enemy helos will appear so find cover and shoot the gunners or the pilots. Once a helo crashes down to the train car you're in, quickly head to the next train car.
Continue fighting your way through the train cars until you finall reach the very first car where Rorke is located. Breach the door and kill the two enemies. Another one will appear from the far end and will fire an RPG, causing you to slide down the floor into the next room. You'll grab Rorke by the throat and you'll be in another slow-motion sequence where you need to shoot the remaining enemies in the cockpit.
After getting derailed, you'll find yourself sinking in the water. During this QTE sequence, you'll have to load the magnum with the last bullet you have and shoot Rorke with it. Water will break in and once you regained control, grab your brother and swim as fast as you can towards the surface. Drag your brother as far as the game will allow and watch the Federation fleet offshore get eradicated in a flash.