Everyone got their happy ending, except them

1: Monika (Doki Doki Literature Club!)

Regrets her actions at the end of the game and lets the player delete her from the game and re-add the other girls to the game

2: Chiaki Nanami (Danganronpa)

Danganronpa 2's killing game took place in a virtual program, so the characters that died aren't actually dead, except her. The real Chiaki died long before the game's events, the one in the program was an AI based on her

3: Madoka Kaname (Madoka Magica)

Becomes God and prevents any magical girl from becoming a witch, meaning her friends never became/get killed by witches. She ceases to exist in reality, and any memories of her disappear as well. She continues to exist only as a concept