He is deemed a High Value Target (HVT) by Task Force Mako, and he is shot in the upper shoulder by Tiger 12, a sniper of the Naval Special Warfare Group under orders of General Barrera. He is presumed dead by both sniper teams, but he is seen still alive after he falls to the ground for a short time.
Four weeks after al-Khalifa gets shot, he reappears (chronologically) in a cutscene before the mission Hot Pursuit. There, he is inside a train as it passes by the train station Preacher is visiting to meet up with his wife and daughter. He stares at Preacher for a few moments before he blows up the train, killing himself and 35 others.