Tear Jerker / Zero Time Dilemma

All spoilers are unmarked.

• Phi's death, should you choose to not pull the trigger in the Incinerator room. What follows is a very heartwrenching scene, in which Sigma pleads for Zero to spare Phi, who tells the two that she loves them and believes they'll meet again. Immediately after, the incinerator door opens. Diana and Sigma walk in, to find nothing left of Phi but her brooch and a pile of ash. Becomes Harsher in Hindsight when you realize that Sigma and Diana had to watch their own daughter die. Because of their son, no less.
  • Another extremely heartbreaking scene occurs in the Incinerator Room, should you choose to pull the trigger when there is a live bullet in the gun. Sigma is killed. Phi screams at Diana for being a murderer, before breaking down into tears (a first for this character). Then, to top everything off, Diana takes the gun and kills herself, leaving Phi alone.
• In the timeline after D-Team solves the Healing Room puzzle, Sigma and Diana are talking when a mysterious figure appears. Said mysterious figure sneaks up on the pair and attempts to stab Diana, only for Sigma move in the way at the last second and get stabbed himself. Sigma tells Diana to run off, and get Phi. When Phi and Diana return, Sigma is laying in a pool of his own blood, near death. Diana rushes to his side, and Sigma misidentifies Diana as Luna. Sigma's last words are an apology to Luna, Kyle and Lagomorph, since his death means they will never be born.
• If you inject yourself with Radical-6 after the Biolab, then Eric recounts his rather sad origin story on his life's outlook, which explains a lot of his horrible behavior towards Q, who he may see as a Replacement Goldfish for his younger brother, Chris, who died at his father's hands. This is made even worse as shortly afterwards, Mira callously disregards the whole story as a joke and then kills him and wounds Q.
• In "Pop Off", Eric's trigger is revealed: strangulation, the method of which his younger brother was killed by. The sight of Mira dead by strangulation spurs him into a rampage.
  • When he demands that Q reveal who did it, but he does not know, it is very hard to watch an innocent little child break down in tears, only able to helplessly repeat, "I don't know!" And to make it worse, if you want the innocent little child to live, you have to make him answer this way, as any other answer will cause Eric to shoot the kid dead.
    • It's telling that the sight of Q on the floor, crying in fear because he genuinely doesn't know who killed Mira, is actually enough to make Eric calm down a bit and apologise, before crying and confessing that he was going to propose to Mira before all of this happened. As terrible as they both are, Eric really does love Mira, and he really does believe that his life is a lot better and happier now that she's in it (with Eric, of course, not realising that she doesn't love him back).
• In "Triangle", the Dramatic Irony of realizing that with Eric's last words forgiving Mira for killing him and asking her to smile, Mira then saying that those words were exactly the same as her first kill, and Eric revealing that those words came from his mother on another Q-Team room... Mira's first kill was likely Eric's mother.
• C-Team's Decontamination Room fragment has Junpei reveal he's seen some pretty terrible things in the past year as a detective.
• That poor jogger whose murder is the basis for Zero's story. Her death led to many other deaths and unfortunate situations as a result. And we learn that before we learn that she forgave Mira for killing her and only asked Mira not do it again.
• The D-2 ending, possibly one of the saddest and most harrowing sequences in video game history. Diana's slow breakdown to becoming suicidal is played out. There's a Hope Spot when Sigma can comfort her, and she has twins, but then the truth that the transporter can only take 2 people and they will starve before it recharges. Although clones of infant Delta and Phi make it out, Diana, Sigma, Gab, and 2029 Delta and Phi are all doomed to starve to death. It's hammered home with one simple line.
  Sigma [to Gab]: That biscuit I just gave you? That was the last one. Thank you.
  • This question Diana asks Sigma. Which is both tragic and ironic knowing what happened to Diana in the timeline leading to Virtue's Last Reward.
    Diana: You won't disappear, will you...?
• The moment in the D-1 ending when Sigma stumbles into the lounge minus two arms and one eye, and he, Phi, and the player all realize the same thing. You have failed.
  • To rub more salt on the wound, the Post-Apocalypse files you unlock from getting the ending details Diana's last moments alive with the younger Sigma in VLR's timeline three years later. It's short, but absolutely heartbreaking, knowing this event is what causes Sigma to create Luna out of grief and loneliness.
• In the timeline where Junpei is killed and dismembered, the ensuing fight between Akane and Carlos ends this way no matter who you decide killed Junpei. If you choose Akane, then Akane slices Carlos' left arm off, forcing him to kill her in self-defense with an axe to her throat; Carlos is not happy with this outcome at all. If you choose Carlos, then Carlos commits suicide out of the fear that he isn't in control of himself anymore after Junpei's death; Akane, having seen SOMETHING off-screen, immediately switches to concern and then regret that she accused Carlos of killing Junpei. The last words before fade to black? "You couldn't have..."
• In C-1's ending, a carefully crafted Hope Spot appears when Akane and Junpei reconcile and become engaged and C-Team gains X-passes through SHIFTing... only to discover X-passes don't work across world lines. Worse, though they manage to SHIFT to another timeline, they've failed to stop Radical-6 from getting out. Though Junpei offers to help Akane, Akane uses the memory drug on Junpei and declares she'll do everything it takes to make next time a success, thus putting them on the path to Virtue's Last Reward.
  • Notice that during the ending scene of this path, the camera focuses on Akane's engagement ring while she declares that she'll never forget Junpei, who will soon have forgotten about her after she injected him with the memory loss drug. Even after 45 years, she's still wearing that ring on her right hand as seen during Virtue's Last Reward.
• The Monty Hall section/the Control room. C Team is stuck in the room which is rapidly filling up with carbon dioxide gas, thanks to a fire started at the end of the puzzle section. Unfortunately, it doesn't stop. Even if you choose the right locker containing the oxygen mask (as per the decision game rules), there's only one, and three members of the team. The fact that neither Junpei nor Carlos hesitate even for a moment to give the mask to Akane makes this something between a Tearjerker and Heartwarming. Junpei didn't even have to ask the question before Carlos agreed.
• A small one in "Reality", if Q chooses not to push the button. This results in Sean getting permanently deleted in this timeline, and is one for both Sean and Zero. Sean, who has given up on life upon seeing that just about everyone is dead on this path, and Zero, with that tone of resignation in his voice upon seeing that he has failed in one of his goals: allowing a copy of his old friend to live his life that was unfairly taken away from him.
  • Then we find out from Zero if you push the button that the real Sean never laid blame on anything for what happened when he was unable to have his operation (Zero implying by 'the coincidences that piled up' to have been referring to the surgeon that died in a car accident). For context, the real Sean was only ten when he died, so the idea that a young child accepted the fact he was going to die so easily is heartbreaking.
  • And then there's Zero's variance of his normal "Life is unfair" ("Life was unfair") when describing the time he spent getting to know the real Sean, who impressed Zero with his intellect enough to offer him a job once he was cured, only for Sean's chances for a future to be lost after his surgeon died.
• Gab's death. It doesn't last very long and he's back before you know it, but seeing an old dog that you've gotten attached to shot to death hurts.
• The realisation that Eric is hopelessly, terribly in love with the woman who ruined his life just makes his whole character arc equal parts tragic and pathetic; even the Golden Ending shows that he never stopped loving her, even after he finds out that she's a serial killer who murdered his mother, and also that she murdered him in the same way in another history. He just accepts it and forgives her for everything.