Spoilers are unmarked per wiki policy.
Even though Zero Time Dilemma has probably the most bloodshed in all of the series, it's still not devoid of moments that can make you all warm and fuzzy inside.
- The scene of Diana comforting a depressed Phi before they were abducted by Zero, especially after you learn that Diana is Phi's mother, which neither of them knew at the time.
- The scenes where Akane and Junpei get over their bitterness and bond like in Nine Hours, Nine Persons, Nine Doors are both nostalgic and sweet.
- Special mention goes to Junpei proposing to Akane in one of the game's timelines. While it is foreshadowed by Junpei fiddling with a ring and struggling to confess his feelings, it's still adorable, even as he confuses which hand to put the ring on. The entire moment is an excellently crafted Hope Spot.
- If you paid attention in Virtue's Last Reward, you'll notice that the ring Junpei gives her is the same one she wears as a 67-year old woman. Even after all those years turned her into a cold, manipulative woman, she still loved Junpei the whole way.
- It goes beyond that. She's still wearing it on her right hand. She promised Junpei that they'd move it to the correct hand once this was all over, and she didn't break it.
- The epilogue files. Junpei and Akane planning to marry after they find the religious terrorist Brother foresaw, Carlos reunited with his sister, and Q-Sean helping Mira to undo the damage she's done. After all that bloodshed, the series ends on a positive note.
- Whenever Eric bonds with Q. Despite being volatile and treating Q like utter shit, there are times where Eric wises up and begins to realize just how badly he's been treating the poor boy.
- The handful of moments where Junpei cracks jokes. It's nice to see that for all his cynicism, the old Junpei isn't gone.
- D-End 2: Sigma comforts Diana about their situation, being stuck in the bomb shelter alone for almost a year. Helping her overcome her Darkest Hour, they fall in love and Diana gets pregnant. When the transporter recharges and they could leave, they choose to instead give their twin children a future, even if it means they'll starve to death.
- Their first kiss especially. There's a reason that cutscene is titled 'Silver Linings'.
- After inputting the Force Quit Box's password for D-Team, Diana regains all her memories from the different timelines, most importantly that she and Sigma are Phi's parents. She immediately goes to hug Phi and breaks down in tears, much to Phi's confusion. Moments later, Sigma and Phi also regain those memories, and Sigma immediately understands and joins them.
- In the game's epilogue files: Carlos and his sister walking happily along the beach, and Carlos seeing Junpei and Akane like a brother and sister to him. Plus, Junpei being embarrassed over the fact he's writing a thank you letter to Carlos for being the reason him and Akane were able to become a couple. There's also Junpei and Akane being playful with each other, and them discussing their wedding plans.
- Sigma immediately moving to shield Q from Eric's gun in the true ending. For all Sigma's talk of selfishness, he really does consider A.I.s to be human.
- Even pre-Character Development, Junpei believes that Akane has nothing to do with this Game, and helps her to keep the first one a secret.
- Akane and Carlos striking up a rapport in the 'Suspicion' sequence. Unfortunately, it precedes the crappiest of crap endings, but there you are.
- The scene in the Quantum Computer Room where Zero tells Q about the original Sean as the voice-acting really sells what is essentially an old man reminiscing about his only real friend in life. It goes on to humanize Zero well before The Reveal.
- While this is genuine YMMV, the epilogue files about Q team can be this. Mira, awful as she is, was able to learn some genuine empathy for other people and developed some measure of remorse for her crimes, turning herself in. She also is able to reciprocate Eric's feelings for her, and they're a married couple - the text even remarks that her smiles aren't fake anymore. While Mira can't truly make up for what she did (leading to Sean helping her break out of prison so that they can create a timeline where she never killed anyone), the idea that anyone can still find some measure of forgiveness, redemption and happiness is weirdly comforting, all things considered.
