Heartwarming / Imperfect Metamorphosis

In the main story

• In chapter 21 "Praying for a Miracle", the scene between Sanae and Kanako. Even more because Kanako has to deal with the guilt of causing the events of Subterranean Animism after Byakuren called her out on this.

Sanae blinked. "Wait a minute, you're not...Lady Kanako, are you saying that they were right? But what about all that stuff about Rin Satsuki being dangerous and the Shadow Youkai and protecting innocent people and stuff?"

"Oh, that part still hasn't changed. But still, I can't help but wonder if I'm becoming too used to taking the practical road. As you know, I've always prided myself as a realist, but maybe I've lost a little too much idealism. After all, aren't gods supposed to help the downtrodden and save the wicked from themselves?"

• The fact that Reimu, who here is very close to her lazy, don't-give-a-shit canon personality and hates the politics games going on, accepts to work behind Yukari's back, negotiate with Kanako and generally facing problems, hassles and dangers that she could have ignored if she had just let Yukari and the Ringleaders have their way, all of this out of sympathy towards Rin Satsuki and a selfless desire to help her and Reisen.
  • Even her assembling of her team is very, very heartwarming. While convincing Byakuren was like knocking down an open door, it says something about her the fact that she manages to rope in Kanako or Mima. And unlike Yukari, Reimu never had to blackmail or bully anyone of them into joining in - they all participated willingly.
• Also, the relationship between Reimu and Byakuren, and the way their interactions soften up along with Reimu's Character Development. Compare:

Chapter 24:

Byakuren: Reimu, I'm an idealist. That doesn't mean I'm an idiot.
Reimu: Funny, I thought they meant the same thing.

Chapter 42:

Yukari: Reimu, we must talk.
Reimu(thinking): I'm an idealist, not an idiot, I'm an idealist, not an idiot...

• After they finally are separated, after a lot of bickering, Rumia fully accepts Rin as a friend, in chapter 49.
• Rin befriending Flandre and helping her to control her split personalities.
• Rin's speech to Flandre in chapter 69. Even though Rin has many, many reasons to hate the residents of the Scarlet Devil Mansion, she still tells Flandre that Remilia loves her and that she'll respect whatever choice she makes. Seeing Rin put aside her grudge for her friend's sake is outright touching, showing that she genuinely cares for Flandre as a friend enough to let her go if that's what she wants.
  • Rin even promises that if Flandre ever changes her mind she'll do her best to help her, even if that means dropping whatever she's doing or breaking her out of the mansion.

In the spinoffs

• The entirety of the sidestory A Very Nineball Christmas is composed of this, from the beginning of Daiyousei's quest to get a present, all the way to the end where the she ends up being given the present by the person she set out to buy it for.