Heartwarming / NieR

For a game that slowly deconstructs the standard JRPG fare, there are a few moments that will make you smile in earnest.
  • Nier's reaction to Emil's new form. It's basically a floating skeleton in a garb with a metal staff. And it looks pretty terrifying. Yet as Emil covers his eyes to sob, Nier walks over and lets the poor kid cry into him.
    Nier: Welcome back, Emil. You've been through a lot.
    • When Popola informs them that the villagers are scared of Emil's appearance and don't want them into town, Nier is pisssssed.
  • One sidequest has Nier and Weiss investigating a missing dog for an old man dying of sickness. During their banter Weiss starts wondering about his own mortality. Nier comfort him that he is made of paper and can't die of age which convinces Weiss. then they find the dog dead with a herb in his mouth. The dog has been fetching that herb every day for his master to treat himself. The old man passes away before they come back and Weiss assumes he is with his dog now.
  • Reading about Kainé and her Grandma. The old lady doesn't care about what Kainé is; she's her granddaughter, and she loves her.
  • The Fisherman's Gambit questline, with an old man who trains you how to fish, despite ridiculous requests and bonkers methods he teaches you. The fact is he was a dreaded mercenary before he retired who, thanks to you, is enjoying what remained of his life after living along for so long until he passes away peacefully, according to a villager.
  • Doubling as a Tear Jerker, Ending D. Nier gives up his own existence to save Kainé, in an act of pure, selfless love. Even Tyrann, who up until that point had been nothing but a remorseless psychotic thug, tells Nier that he's giving up his life probably for the same reason Nier is, implying that despite his truly awful nature, he had grown attached to Kainé in his own way and so was willing to make the same sacrifice.
http://tvtropes.org/pmwiki/pmwiki.php/Heartwarming/Nier