In chapter 4, Derpy sees her daughter being abducted by the griffins, but still tries to save her despite being wounded. She fails and breaks down into tears. By the end of the chapter though, she manages to rescue Dinky though with the help of Mirage squadron.
In chapter 6, Rainbow Dash goes solo to rescue Applejack from the griffin claws. She finds her beaten to a pulp and pinned against a wall of ice, completely helpless. When she frees her, Rainbow is horrified upon seeing the pain Applejack went through. The fact that Applejack tries to play it cool makes it more heartbreaking, as she realized her folly, and if it wasn't for Rainbow, she would most likely end up dead.
Firefly's backstory in chapter 8. When she returns home to find it engulfed in flames, she learns that her parents were killed by Black Star (who openly admits that he killed them). She tried to fight him, but was effortlessly knocked aside. As he was leaving the battered and beaten pony, expressing hope to meet her again, she burst into tears not only mourning for her parents, but also in lament over her dreams of becoming a member of the Wonderbolts being crushed all because of this one encounter. You can't help but feel sorry for her.
Worst yet, her parents' deaths were deemed as "unfortunate accident" because both Black Star and Firefly left the scene before any authorities arrived.
Firefly's pain experienced upon meeting him again after five years in the previous chapter.
When Fluttershy (unintentionally) kills Razor during the mission to destroy the Burning Talon in chapter 10. After it's destroyed, she stares in disbelief at the burning ruins of the superweapon, mumbling: What.... what... wh-what have I done? What have I done...?. Upon returning to Canterlot with the others, she retreats into Mission Control, where she cries alone. After Rainbow Dash tries to talk to her, she repeatedly blames herself for killing a sentient being (a villainous one, but sentient nonetheless).
Doubles as Heartwarming Moments when Rainbow and the rest of the Mirage squadron try to comfort Fluttershy. Bonus points for Cloud Kicker thanking Fluttershy for saving her life, which was the reason Fluttershy fought Razor in the first place. Then Rainbow Dash asks her if she wants a hug. Out of pure emotion, Fluttershy embraces Rainbow Dash and cries her eyes out, saying with a choking voice: "Im sorry! Please, forgive me!".
The ending of chapter 11 is pretty heartwrenching.
Rainbow Dash drowns herself in despair while resting in the hospital, refuses to help others in defending Stalliongrad, continues to curse herself. Firefly bursts out of the room after the rest of the Mane Cast visit her; Applejack's sadness upon being unable to help Rainbow Dash as she helped her before is crushing. Just to drive the point home, when the ponies are leaving, Fluttershy practically begs Rainbow Dash to get better and kisses her forehead, saying they will be waiting for her. This cures Rainbow Dash of her catatonia, but makes her break down again. Outside, Firefly stands soaking wet in the rain as Lightning Bolt calls her out for berating Rainbow. She suddenly yells at Lightning, telling her that she's wrong and that she does care about Rainbow Dash and her friends, but seeing her in such broken state reminded Firefly of her own Dark and Troubled Past. Thankfully, things get better afterward.
Chapter 15. Dear Celestia, chapter 15. A massive Drama Bomb to begin with, but in order: the griffins have invaded Canterlot and seized the city, the castle being the only save place now. Many ponies are injured and some were killed during the raid. Tornado Swirl and Overdrive lost their entire squadrons, with Sea Spot having performed a Heroic Sacrifice to save Overdrive. The Stingray team was wiped out completely. Then, when Fluttershy asks about Blueberry's fate, there is a slight Hope Spot that she could have survived... but then Flare Star comes in and reports that Blueberry died , but went down in a blaze of glory. Moments later, it is revealed that, on their way from Trottingham, Flare Star's team was intercepted and she lost one of her wingmares... who happens to be Raindrops, one of Derpy's best friends. That's not all of it, though. Carrot Top was recovered from the battlefield, mortally wounded. In a truly heartbreaking manner, she tells Derpy to keep on living and survive the war before dying peacefully in Derpy's arms, smiling until the end. Derpy breaks down in despair, later bidding a touching farewell to Carrot Top before going to see Dinky. And this is just the first half of the chapter.
In-Universe, this situation is so depressing that even Cloud Kicker, established as being the most cheerful pegasus among the main heroes, lets her water works completely loose. Not only because she is saddened by the other ponies' deaths, but also because she fears her best friend may die as well.
Cloud Kicker: (sobbing) I-I-Im scared, Lightning! Terrified! So much death... I feel s-s-so sa-ad... Nopony deserves t-that much suffering... What i-i-i-if... What if you die, too? I... I dont think m-m-my heart could take i-it...
Shamrock telling Fluttershy about his dead little sister. And because he witnessed Carrot Top's death, it only reminded him of Morning Glow. He additionally blames himself for not saving Carrot Top. Having a chance, he instead went to help the pegasi. Fluttershy manages to snap him out of it, but still.
Shamrock: Im no angel... just a weak pegasus pretending to be one... I failed again.
Finally, Derpy having to tell Dinky about Carrot Top going into the Big Sleep. Despite hearing that term, Dinky understands that she has passed away.
Dinky: Mommy... is auntie Carrot... dead?
At this point, Derpy, emotionally exhausted, shatters completely for a while.
The author himself confessed he suffered from mild depression while writing this chapter.
Firefly going through a crisis in chapter 16. It turns out the reason she was sometimes cold and apathetic towards the other ponies was due to losing her family. After Princesses Celestia and Luna make her realize that, they additionally state that even though they can raise the sun and the moon, they are unable to revive the dead. Hearing this, Firefly starts shedding tears.
Firefly: Mom... Dad... I miss you... I miss you so much...
The scenes in Garden of the Fallen in the epilogue.
Ace Combat: Wings of Unity
How to amp the drama when compared to previous story? How about having the town of New Saddle being completely destroyed and making a BABY PONY one of the victims?
The worst thing is that everypony believe that the little pony is just uncouncious... that is, until its mother starts crying. Medley, who pulled it out of the ruined house, breaks down soon after.
Firebolt's death in chapter 6. And pretty much the entire dialogue between her and Spitfire after Firebolt is shot down.
Chapter 7 is called "Mourning" for a reason, as it deals with Spitfire coming into terms with Firebolt's death. It's quite heartwrenching to see a tough mare like Spitfire being on the verge of breaking down. Rainbow Dash eventually helps her, but her confessions and guilt make it clear she's been greatly affected.
This particular moment, after Spitfire experiences a Flashback with Firebolt telling about her reason of joining the Wonderbolts:
Rainbow Dash: Spitfire, are you alright?
Spitfire: Rainbow... Can you... do me a favor?
Rainbow Dash: Sure... Anything.
Spitfire: Hug me... Please...!
Suprisingly, Pearl Eyes's lamenting to Bolt Burst by the end of Chapter 10a gives quite a sympathetic vibe to her. All she wanted was to obtain her first victory in battle, but Flare Star made sure it would not happen.
What happened to Pearl during the battle wasn't pleseant either...not only did she come within a hair's breadth of being killed, she was reduced to pleading for her life (which Flare Star ignored) and humiliated as a rookie. Mook or not, she likely won't recover from this for a while...
Rumble and Scootaloo, maybe. But Dinky certainly not. She is still in a mild shock after the operation until the other Crusaders cheer her up.
It's brought up in chapter 11b, when Dinky says she won't partake in killing other ponies because of how the death of an Exile soldier traumatized her.
And AGAIN in Chapter 12, when Dinky tries to explain why they agreed to partake in the operation. Then she hugs Derpy and starts crying and all she can do is try to calm the little filly down, saying she did nothing wrong.
In chapter 11a, Tornado Swirl and Overdrive are trapped by Orgoi's ice magic and they are fully prepared to face death together. They are luckily saved due to Viper squadron's arrival, but for a moment things looked very bleak for them.
Later, Orgoi makes a terrifying display of his powers by annihilating most of Quox's battalion, leaving the poor mare in a state of mental breakdown. Then he starts eliminating members of the Viper squadron, killing four fliers in a brutal fashion, with Lightning Dust being unable to prevent them from dying.
After the operation, Lightning Dust is deeply affected with the loss of her wingmates, but by the end of the chapter, the remaining pegasi from her team try to cheer her up and say that they will stick with her and help her, calling themselves her friends. Lightning Dust's first reaction is disbelief... then a great relief, as she no longer hides her tears.
Lightning Dust: (stammering) Friends...? Heh... that sounds cool. I guess... I do have... friends...
The moment mentioned above becomes additionally sad when in Chapter 12 Lightning Dust leaves the EAF, upset about being treated like a scapegoat and delinquent (however rightfully). Her friends try to stop her, but fail.
Sundance's reaction is especially heartbreaking. She tried to hold onto Lightning Dust, but gets knocked down to the ground. She's so upset all she can do is whimper.
Rainbow Dash's crushing defeat when fighting alone against the Reaper squadron in chapter 14. She is completely outmatched and powerless against the Zeal-powered Reapers and suffers a No-Holds-Barred Beatdown that makes Gilda's beating from the first story seem tame. At the end, she suffers from a broken arm, ribs and several other injuries. As she is losing conciousness, her thoughts get more and more desperate, looking like she may end up dying.
Rainbow Dash: Is this it? Am I going to die ? No I I dont want to Girls ! Fluttershy Firefly Applejack Twilight Pinkie Rarity... Medley... I... Somepony Anypony Please... help me Please !
Medley breaking down in the following chapter, as she slowly begins to realize that Rainbow Dash can, in fact, be dead. Upon returning from an unsuccessful search, she blames everything on Firefly, letting her emotions loose and screaming that she hates her.