Complex sentence: Throughout the patrol period, mission readiness was tested by emergency action messages being sent to ship many of which would result in full crew participation with sounding of the General Alarm followed by Man Battle Stations, Missile.
Split into simpler sentences: Throughout the patrol period, mission readiness was tested by emergency action messages being sent to the ship. Many of these EAM's "would result in full crew participation with sounding of the General Alarm followed by" Man Battle Stations, Missile.