The whole game is one long one, but the ending scene takes the cake. Other than the scene where Everything's Alright plays.
Alternate!River reaches out her hand to Alternate!Johnny, and Johnny turns around and takes her hand. Everything you've been doing for the past 5 hours comes to this point. And you just break down at that moment. And then the montage of Johnny's new memories rolls, of his wedding to Alternate!River, building their house, growing old together, this time with Joey along with them. At this point you are consumed by grief and joy and hope and despair and guilt and so much relief that you just want to find the people you love and hold them tight.
When you realize that River made those paper rabbits to remind Johnny that they are supposed to meet on the moon if they ever get separated. Only Johnny can't remember that memory because of the beta blockers. But River doesn't tell him of their very first meeting. Why? Who knows. Maybe because she didn't want to remind Johnny of his tragic past. Maybe her Asperger's prevented her from fully communicating with him. All we know is that she diligently and quietly folded those rabbits, trusting him to understand what she meant. And then she died. But Johnny finally fulfills his promise before he died. Maybe. In a way. It was artificially implanted, but it was still real to him in those final moments of his life. Maybe. The only comfort you can take away is that he died happy and doing what he promised, only he didn't really do it. When you realize all this it just breaks your heart into pieces.
The reason why is fairly clear - River was never aware of WHY Johnny forgot his promise, along with her. Her condition was the reason she never asked outright, but she was never aware of what had happened to his brother, because by the time they reunited, he'd had that memory suppressed. On top of that, this adds a huge dose of Fridge Brilliance to what she said at the movies - that she believed that they were watching it together without being physically near each other, just as she'd probably done the next year at the carnival. All that grief because of one tragic event...
He DID remember his promise! He still remembered to go to the moon. He just forgot why.
YMMV, but what's worse is that all of River's efforts to make Johnny remember the very first time they met, it became completely pointless when all the memories were remade to help Johnny's desire to go to the moon. To those that wish that Johnny at least remembered his true memories felt like a Kick the Dog moment in her part.
And of course, the scene with the Award-Bait Song "Everything's Alright", in which we get to see all of Johnny's memories with River get erased and rewritten so that he'll be driven into going to the moon to fulfill that half-remembered promise. The song itself is rather heart-breaking, what with its references to River's Asperger syndrome.
Why do my words Always lose their meaning? What I feel, what I say There's such a rift between them He said, I can't really seem to read you." I just stood there Never know what I should do.
The implication during The Stinger that Neil might be dying. It becomes even MORE depressing when you realize why he acts immature, mean, jerkish, and does stupid ridiculous things. (like riding a horse backwards) He's trying to get the most out of life before he dies...
Or he's just addicted to pills and is going through withdrawals. Very easily that's just as bad if not worse.
Why does River care so much for Anya, a lighthouse of all things, so much that she is willing to die instead of letting it be alone. Because when they first met, River called all the stars lighthouses that could never reach out to anyone and were always alone, but that one day she wanted to befriend one of them. The implication being that she herself no longer wanted to be alone either. And then you can demolish boxes of tissues when you realize exactly why she asked what she did.
The hackey-sack. It was given to River by Johnny when they first met, but Johnny no longer remembers the event. When he reveals to River the reason he approached her during "their first meeting", she asks him to throw away the hackey-sack. It was probably around then that she realized that he had forgotten about their REAL first meeting. It makes everything afterwards so much more bitter in hindsight.
Particularly when you realise she didn't actually want him to throw the hackey-sack away. She was trying to use it, along with the concept of "a far distance" (as the moon is far away) to try and trigger his memories. He didn't understand her action and she lost a memento of their first meeting as a result.
When Johnny is discussing what he likes about River, his only attraction to her is how she is strange and different from everyone else. And all he knows is that he WANTS to be different, but he can't put why he feels so exactly into words. At this point he has lost his memories of his twin brother Joey, but his mother still calls him by that name and he most likely subconsciously wanted to stand out and not be seen as a replacement. Perhaps even worse is how different this "first meeting" of his with River is from their real first meeting.
The Reveal, when you discover Johnny and River's true first meeting, is so beautiful, tragic, bittersweet, adorable and magical, it would probably be the first point you start crying if you had been holding back tears before this.
And, as noted on the main page, a number of Chekhovs Guns get pulled at once during this scene.
And there's a major one just after players see River for the first time, when Johnny is sitting at their half-finished house on the bluffs and having a dramatic conversation with Izzy. When she criticizes his decision to lie to River for her own health, his retort is heartbreaking.
Johnny: Do you think this is all about her? What about me, Isabelle? After all these years, am I not allowed to be selfish even once? ...I don't want to be alone, Isabelle. I'm not going to let her die.
Izzy: That's arrogant.
Johnny: I don't care.
Isabelle's line about neurotypicals forcing their views on others can sting quite a bit for neurodivergent people who have gone through being pushed aside.
Adding to the sting for Johnny is an inadvertent ironic gift - a music box that plays "Everything's Alright". As Johnny bitterly says - "It isn't."
It's easy to forget this given the backwards linear path of the game, but the house was finished being built only after River died. Despite that, Johnny still keeps all the clocks silent, because the ticking bothered River.
Johnny's entire childhood can be considered a montage of Tearjerkers. His mother favored Johnny's twin brother, Joey, and the father is never seen, or even brought up. And that is before Joey's death.
Joey's death. It's obvious that despite the parental favoritism, Joey loved his twin brother, and wished for both him and their mother to be happy. His death is too simply too cruelly ironic in nature, as it's Johnny's mother who accidentally ran Joey over. However terrible a person Johnny's mother may be, one can't help but feel absolute pity for the shock and guilt she must have dealt with afterwards.
Colin's reasoning for wanting to become a pilot, as related to Sofia, and directly referencing the events of A Bird Story.
Colin: ...A long time ago, a friend of mine went somewhere far away. I guess I just... wanted to go find them again.
Fulfilling Colin's wish turns out to be relatively easy, when all's said and done - just remove the memories of Sigmund, so that he won't dwell on What Could Have Been. Thanks to this, he got to have a final conversation with Faye so that he can say goodbye properly. That was all he wanted, but couldn't say so due to her being his Imaginary Friend.
Preceding this, though, Colin dies in his sleep... with his wife, Sofia, kissing him on the cheek and embracing him as the EKG flatlines.
This is made Heartwarming when we see Colin's memories - his final thought, framed side-by-side with Sofia's actions, are to kiss his sleeping wife's forehead just as she kissed his.
For that matter, the center of the "vortex" in Colin's memories - the moment he had to say goodbye to Faye, his only friend throughout childhood, as she was imaginary and she (or rather, they both) decided it wasn't healthy for him to keep holding onto her, as it was allowing life to pass him by. In the lead-up, Colin is visibly dragging his feet, wanting to postpone the inevitable as long as he can, but the hug at the end is especially poignant, as she sprouts wings to embrace himnote hinting that Faye was directly inspired by the bird he'd adopted so long ago... before slowly fading into nothingness.