I think instead of putting a warning in the title it'd be much better to just spoiler your answer and mention what game it is.
There is only one appropriate choice for me.
Metal Gear Solid 3:
So now everything is set for the final battle, the final objective, the face off to prove you surpassed her. All what happened was supposed to lead and prepare Snake to this event. With the 10 minutes Snake had to kill what he considers a mother figure, he managed to knock her out. Hesitant to kill her, The Boss herself had to BEG Snake to do it, telling him that there can only be one boss. Snake kills her, no YOU kill her. You, the player, are the one who pulled the trigger, unbeknown to the truth. The battlefield, a flower garden, turned red in response to her death, and the agonizing Snake-shaped scar she had that symbolizes her giving birth in the battlefield, left and disappeared, indicating she finally found peace.
But that's not what so sad about this - Hear me out. After the Operation was over with, Snake wakes up with a voice message from Eva, his lover, and the only one who knew the truth about The Boss. What's in the message is Eva admitting that she was actually a spy for the Chinese and the real reason how she knew about The Boss was the she was her teacher when she was younger, and then the real reason behind The Boss's defection. She was actually forced to defect to act as a spy and to obtain The Philosophers' Legacy, and that no one should know this. But things happened and Volgin bombed a facility in Russia, and a controversy happened where in order to prove that America wasn't responsible or affiliated with this, they had to kill The Boss. She couldn't commit suicide, she had to actually get killed, and she didn't hold back against Snake because it would be considered suicide if she did. She had to trust her student to accomplish his mission. It wasn't suicide, it wasn't murder, it was sacrifice.
She died for her motherly love to Snake, and honor for her country. Snake knew this. Everyone in both Russia and America view her as nothing but an enemy and a villain, when she was the real hero. Snake knew this. She had to trust her own student to accomplish his mission, kill her and become an entity above her. Snake knew this. And he doesn't view himself as the hero after this, but she was still the real Boss, the real hero. He doesn't think he deserves the title of "Big Boss".
Really the only death scene I ever felt actually touched me. The song played against the character was so fitting too, it pretty much tells the whole story about the scene.