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Tear Jerker: Virtue's Last Reward
Learn about Tenmyouji's past and identity, then just try to maintain composure when you realize the identity of the old woman.
"The Akane Kurashiki I knew isn't there. She isn't anywhere..."
In what doubles as a Crowning Moment of Heartwarming, the password of the old woman is Jumpydoll. "Jumpy" was Akane's nickname for Junpei when they were children, and her most treasured possession was the doll he gave her as a parting gift. Akane never forgot about Junpei, even after all those years.
Luna's ending, especially when Morphogenetic Sorrow (the theme of the final puzzle from 999) begins playing during a flashback.
Luna: I watched six people die and did nothing. I deserve this.
Sigma: No! No you don't! Even if you had done something, you would have been killed anyway! You can't blame yourself! You did what you could, you're not wrong! The game is what's wrong! Forcing you to watch your friends die is what's wrong!
Luna: Oh Sigma... Thank you. I'm... I'm really glad I met you... At least I get to die in your arms...
Even more so when you look back to K's ending: K was saying how Zero Sr. created a "robot mom" for him. That robot's/GAULEM's name was never stated in K's ending, but is confirmed by Word Of God to be Luna. Suddenly "It looked sad, but it was only programmed to look that way" from K doesn't sound so convincing anymore... And part of the reason for Luna's loneliness is explained.
What about Snake? Clover's esper abilities are being absorbed by the other, more powerful psychics in the group, not to mention she's forty-five years ahead of him, assuming he survived the Radical-6 outbreak and the antimatter holocaust. To him, his sister blinked out of existence one day, never to be seen again. Even if the events of the End or Beginning path come true... what about all the other Snakes whose Clovers never come home?
The Game Over cutscene of the Normal End of the game if you fail to disarm one of the bombs. Right as the bombs are about to explode, Phi falls into your chest and thanks you for always standing by her, while Sigma vows to go to the past and make things right.
The K ending. According to Word Of God, K, who on this path is Sigma's clone/son Kyle, was the one who broke Dio's bracelet, preventing himself and Phi from going through the white door. He knew that Sigma, his father, would only be able to save one of them from the bracelet penalty with the neostygimine, and wanted to see if Sigma would choose him, even knowing that Sigma's 22-year-old consciousness would not remember him. But Sigma chose Phi. Even though it was apparently out of necessity, since Sigma didn't know that K's armor was unlocked, one can only imagine how that made Kyle feel.