Disable the Security Panels / Steal the Patrol Boat
Once you’ve activated the mission via the planning board on the Submarine, either use the sub to fast travel closer to the Merryweather HQ or simply drive there yourself. After you’ve arrived at your destination, take cover and take out all the Merryweather Soldiers, then interact with the Security Panels which are located on the ground floor and second floor.
Upon disabling all the security panels, head up the stairs at the back of the warehouse and interact with the main terminal to open the gate. Jump in the Patrol Boat and race toward Los Santos International Airport. Exit the Boat and use a homing rocket launcher to take out the helicopters, then deliver the boat to the hangar.