- Elisa's death. She's in her early teens, has an obvious crush on Naked Snake, and is seen by him as almost a daughter figure, considering how freely he talks to her about himself. Not to mention her vision of Big Boss' future, complete with foreshadowing of what happens in other games of the series. Double tear jerker for fans of the entire series, compounded by the beautiful, haunting tune of "Calling to the Night."
Elisa/Ursula: The futures we saw were one and the same. Snake, you will destroy Metal Gear and you will create a new Metal Gear in its place. Your children...Les Enfants Terribles. Snake, your son will bring the world to ruin. Your son...will save the world.Snake: What are you saying, Elisa? ELISA!!!
- Snake telling Jonathan about his mentor.
Snake: She died out of loyalty...not to justice, not to her country, to herself. For the mission.Jonathan: Your mentor...the one who taught you the art of battle...who was she?Snake: They called her The Boss. I killed her.
- The death of Jonathan. The cold, matter of fact message you get after is just heartbreaking.
- Jonathan has died.
- The potential death of Python, Snake's old war buddy.
- The music that plays during the battle with Gene is quite sad. Probably because it takes place right after Elisa's death.
- See the Mauve Shirt entry for another.