First method would be to try and complete all four of the Emergency Orders through out the stages. This unlocks the secret mission at the end, make sure you shoot down the nuclear missiles or you get ending B, if you succeed and shoot all the nukes down, then you will receive ending A. To shoot a missile down, you must use your cannons, missiles can not hit them. Use Climax Mode to slow down time so your shots are more accurate.
The second method is to complete 20 Emergency Orders, this will unlock an Ex Option which allows you to set the secret mission to always available. Simply play through and when you get to the last stage (14), make sure to shoot all the nukes down. See first method for details.