After several restarts I'm still not getting it? Any help would be great! BTW half way into the mission the "orders" change, put out the fires & moves pilots to safety... I can't figure this one out.

Use sniper mode. At almost every corner is a wall of rubble. Use the sniper rifle against all enemies. It's time consuming but really the only way to get through. If you do it right the enemy can't even shoot at you! There is a leaking pipe in with the soldiers that you are trying to resque shoot the pipe in sniper mode and everything will become clear.