The story had its share of nice moments, but it was chapter eight that was by far the most heartwarming chapter.
Despite that Rainbow Dash is oblivious to Fluttershy's feelings throughout the story, even her own; it's pretty clear that if she was more aware of how love (and even sex) worked, she'd be in love with Fluttershy.
Chapter seven had filly Rainbow Dash proclaiming her three favourite things. Athleticisim, the Wonderbolts, and Fluttershy. What made it cute was that she sweetly suggested to Fluttershy that she become all of those things, so that she would be all of her favourite things in one package. It was called back to in-universe in chapter eight. The callback was even done word-for-word the way filly Rainbow Dash said it, making it even more adorable.
Rainbow's genuine remorse in her explanation to Fluttershy as to why she left Cloudsdale, and why it was hard for her to tell her about it back then. Despite that she ended up getting where she wanted to be in the present time, it came at the price of leaving behind her best friend; something Rainbow admitted was the hardest thing she'd ever had to do. While she admitted that she would have chosen Fluttershy in a heartbeat if she DID tell her; Rainbow does not say it in any kind of resentful way, but more out of regret. It shows that even though she knew that, she never held it against Fluttershy.
Rainbow and Fluttershy's hug in chapter eight after they'd finally reconciled. Pinkie Pie and Rarity letting out a "D'awwww" chorus pretty much sums up how the readers must have been feeling.
Fluttershy accepting that she not only never fell out of love with Rainbow, but that she fell in love with the best mare she could ever ask for, twice. Everything made her fall in love all over again, and this time, she is no longer afraid of her feelings.
At the end of chapter eight, Rainbow and Fluttershy try to fall asleep, but are missing each other. This is remedied when Rainbow goes to Fluttershy's cottage, is kicked into the room by Angel, and they fall asleep together. Despite the tough aspects of being bound together like they'd been; their closeness definitely meant a lot to them.
Despite the tension between him and Rainbow, Angel kicked Rainbow into the room so that she could sleep with Fluttershy in her bed. After everything that happened, after all of his attempts to break them apart, he relented to let them be together. He realized that Fluttershy felt lonely without Rainbow around, and that he himself was bored. He may have been a jerk throughout, but he does care about Fluttershy and wants to make her happy.
Throughout the story, Pinkie makes it no secret that she wants Rainbow and Fluttershy to get together. Despite her attempts being unorthodox and silly, she does care about them and just wants them to be happy.
Although chapter seven was a bit of a tearjerker throughout the backstory exposition; the adorable moments between filly Rainbow and Fluttershy were so sweet.
Even Souldin's thanks to all who read and commented on his story deserves a mention of its own.
Despite the intensity of the scene, Fluttershy's reveal of why she named her pet bunny Angel is really sweet. She named him Angel because he reminds her of her OTHER Angel; Rainbow Dash!Wordof God has stated that it is in reference to a short fan art comic of that same idea.
Although it's begrudging, Rainbow and Angel's moment of reconciliation is about the closest they will get to some kind of a agreement. Oh yes, they still don't like each other, of course; but it shows they're willing to put their differences aside for Fluttershy's sake. They both can agree on two things; not to speak of that moment again, and that they care about Fluttershy. After everything they'd done to one another, it's even nice that they see one another as a worthy opponent.
Rainbow's bathroom emergency in thanks to Angel. Although Fluttershy has no choice but to stay close to her in thanks to the bracelets; it does still help that she's willing to stay by Rainbow's side to help her through it.
In chapter five, Fluttershy is taken along for the ride on a pranking spree with Rainbow and Pinkie. It all doubles as a Crowning Moment of Funny, all things considered. What makes it all heartwarming is not only Rainbow's Friendly Tickle Torture on Fluttershy, but also their sweet conversation before that. Adding to it is a Near Kiss which Pinkie interrupts.
Also in chapter five, Pinkie reveals to Applejack that Rainbow Dash pulled out of doing a certain prank simply because Fluttershy didn't want to. It just goes to show that even before their Crowning Moment of Heartwarming reconciliation in chapter eight, Rainbow did still care about Fluttershy and wasn't about to force her into a situation she wasn't comfortable with.
Despite it becoming an Interrupted Declaration of Love, the moment still counts in that Fluttershy was ready to tell Rainbow how she felt. To truly showcase how she has completely accepted her feelings for her.