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Tear Jerker: Professor Layton
Sophia's letter to Anton during the ending of Professor Layton and the Diabolical Box.
Same goes for the music that plays during that scene.
"My dear Anton..."
Don't forget the images that come with the credits. Mix the pictures of Sophia and Anton's love and separation, Mr. Beluga and Anton's reunion, and Katia and Anton returning to Dropstone and being welcomed back with praise with the music above, and you got yourself feeling like happily crying for a good amount of time.
Nine words do it for this troper: "There's someone I need to get to know first."
Everywhere in the ending Professor Layton and the Unwound Future, but especially during the third-to-last cutscene. "I don't want to say goodbye again! I can't! I won't!" All the more heartrending when you remember Professor Layton usually plays the part of the unflappable, unemotional English gentleman; for that one moment, the mask slips, and you get to see his heart in the process of breaking — and your own breaks with it.
Worse, it's not just that his heart is breaking. It's that he's just rediscovered that the woman he loved was actually alive, just in time to lose her all over again.
Let's not forget that he also took off his hat for the first time in-game ever. The emotion in that scene multiplied leaps and bounds.
As well as Luke's good-bye with Layton. That in itself is sad, but then Luke starts the waterworks. Layton tells him a gentleman doesn't make a scene in public, but Luke, the boy who has always strived his darnest to be a gentleman shouts, "I'm sorry, but I'm not a gentleman yet!" He then leaps into Layton's arms while in fits of tears. After so much of their camaraderie, to see them say "so long" is heartwrenching.
Long story short, the last ten or so minutes of Unwound Future will make you SOB. Klaus/Clive's Motive Rant and saying that he was really hoping for the Professor to save him and that he actually did enjoy their time together.Layton's goodbye with Claire, like the above troper already mentioned. Luke saying goodbye. And if you look closely at that cutscene, you can see that Layton's crying too.
Not to mention the small flashback of Layton holding Clive and comforting him while trying to hold him away from the rubble that used to be Clive's home. "I HAVE TO GO BACK! MY PARENTS ARE STILL INSIDE!" Oh god why.
In Lost Future/Unwound Future, there's one point where Layton is explaining how he kept trying to investigate Claire's death, but he ends up getting severely beaten. The player is then treated to this◊ image. To see the good Professor like that is very upsetting to say the least.
In Specter's Flute/Last Specter: We find out about a giant sea creature named Loosha, a cute giant sea lion who befriended Arianna the so-called witch. It was fighting off the specters tooth and nail all so it could lead Arianna to the Golden Garden to cure her. Unfortunately, all the wounds Loosha took to make sure Arianna could come to the garden caught up with her and she died. Its body then sinks into the depths of the water.
Oh, and one more thing: Loosha was the last of her species, and that fact added to the adorable flashbacks of Loosha playing with Arianna and Tony is just heartbreaking. Made even worse was before finding out about the Golden Garden, Loosha was breaking down the dam and Arianna screamed that she hated Loosha and threw a rock at her...and then instantly regretted it when Loosha lets out her final cry.
The last episode in Last Specter revolves around Chelmey's past. He was a constable and the head inspector was Gilbert who noted that Chelmey would soon be promoted to investigator. Unfortunately, Chelmey was in too big of a rush to bag the criminal and ended with Gilbert taking a fatal bullet for him. Gilbert's last words were about how Chelmey would be a great investigator. His last requests was for Chelmey to never give up on Scotland Yard and live his life. Chelmey felt so bad and keeps screaming "INSPECTOR!" as the flashback comes to a close.
From Miracle Mask, Randall's death and especially its aftermath. Foreshadowed and then openly mentioned throughout the game up to that point, it still hits like a truck. Hershel is utterly broken afterwards, so much that he needs to leave his village to overcome the grief for failing to save his friend.
The BGM Override for the next puzzle (which also happens to be Puzzle #100) certainly helps keep the mood going. It really gives you the feeling that your imminent triumph over the ruins is all too bittersweet.
And what's on he other side of the door? A mountain of gold and jewels. No grand discovery for the progression of archeology. Hershel is seen touching one of the coins, and collapsing in grief.
Hershel: No technology. No magic, Randall. Just this. Gold. Gems. Metal and rocks. Was this worth your life?
From Azran Legacies Descole's (FAKED) death. Many of us guessed it was coming, but no one expected him to basically kill himself. At least he died in the ruins that he was so passionate about, but that doesn't soften the blow... And then he's shown to be fine about ten minutes later. Not quite so sad, but it gave several of us minor heart attacks.
It absolutely DOES NOT help that Descole is actually Layton's brother. Not only that, but HIS name is Hershel, and when his little brother was adopted by the Layton family, he gave his first name to him.
Not only Descole; Layton, Luke, Emmy as well as Bronev sacrifice themself to stop the Azran Dolls. However they all get revived afterward.
Also from Azran Legacies Aryan's death, after her 'role' as Azran Messenger is over.