* The terminal entries left by Granny Smith's boyfriend Hoss, detailing most of the important and personal events of the war, including the deaths of Big Macintosh and Granny Smith. Blackjack and P-21 than bury Hoss' remains in the grave beside Granny Smith.
* The climax of Chapter 6 in the Fluttershy Medical Center, when Blackjack is [[spoiler: [[MercyKill forced to kill 40 foals]] - she doesn't have any option other than [[AndIMustScream leaving them in their pods, insane]]. It gets even worse when, as she shuts the pods down one by one, she starts singing [[IronicNurseryRhyme "Hush Now, Quiet Now"]]]].
* [[spoiler: [[AlasPoorVillain Gem, Mini and Taurus]]]]'s deaths - particularly the brief conversation with [[spoiler: Dying!Mini]] after [[spoiler: Deus is killed]]. Accentuated by heavy MoodWhiplash.
* [[spoiler: Roses']] funeral.
** [[spoiler: Thorn]]'s death and subsequent burial, shortly afterwards.
* The opening scene of Chapter 22. Moments after realising that [[spoiler: [[DoomedHometown Stable 99 has been]] [[TheVirus infected by the raider virus]]]], Blackjack enters a TranquilFury as [[ZergRush dozens of raiders pile in on her.]] [[spoiler: The hopeless battle is described in painstaking detail, as Blackjack recognises - and momentarily reminisces about - each and every stablepony-turned-raider that she kills.]]
* [[spoiler: Blackjack's attempted suicide]] in Chapter 23.
** Consequently, [[spoiler: P-21's attempted suicide]] in Chapter 25.
* Blackjack's reunion with Glory in chapter 25. Glory is initially livid with her over [[spoiler: her suicide attempt]] but gradually breaks down and confesses that, without Blackjack, she had nothing left to live for.
* [[spoiler: Gorgon]]'s [[TragicMonster "i am not monsher but i look liek won"]] letter, and the dark CallBack later on when [[spoiler: Blackjack is deformed by taint]].
* Blackjack's tearful reconciliation with P-21 at the end of Chapter 33, and [[spoiler: subsequently, her death.]]
* Chapter 43. All of it. Everything from Blackjack's heartbreaking refusal to believe [[spoiler: that her friends don't exist outside of her mind]] to her finally [[spoiler: reaching some level of closure with her mom]] to the [[spoiler: abandoned Happyhorn computer slowly trying to comprehend that it can't ever fix her.]]
* [[spoiler: Lacunae's death after the destruction of the Goddess. Being a fusion of all the discarded emotions and memories of the ponies fused into Unity, she performs a HeroicSacrifice and destroys herself to restore the memories of her sisters. Psalm is resurrected as a result, but she is not Lacunae.]]
* Goldenblood and Fluttershy's doomed relationship. During a moment of intimacy, Goldenblood calls out Luna's name (since she decided to have a telepathic chat with him at the wrong moment). This causes Fluttershy to think he is unfaithful, and goes into early labour, and have a miscarriage. Though this obviously turns out to be false since Sanguine saved the baby who became Psychoshy.
* The tragic fates of all of the members of [[TheSquad Macintosh's Marauders]]:
** Big Mactinosh: [[spoiler:Gunned down by Psalm in an attempt to assassinate Princess Celestia, and his death was made to look like a HeroicSacrifice]].
** Applesnack: [[spoiler:Reassigned to guard Zebratown, became the first Steel Ranger, murdered Zecora, broke up with Applejack, and then became a ghoul]].
** Twist: [[spoiler:Raped by Doof, her zebra lover Shujaa is killed and gives her the Phoenix Talisman, trapping both in it. Twist later becomes part of Rampage]].
** Psalm: [[spoiler:Went from a devoted follower of Luna driven by faith to a self-loathing ColdSniper. She carried out Project Partypooper, murdered Pinkie Pie, and was then absorbed into the Unity, became Lacunae, and used as a dumping ground by the Goddess for all the unwanted emotions and memories]].
** Doof: [[spoiler:Manipulated by Brass into raping Twist, sent to Hightower Prison, grew to hate all mares, and eventually transformed into Deus through Project Steelpony]].
** Stonewing: [[spoiler:His death was faked by Sanguine so he could be used for Project Chimera and transformed into Gorgon]].
** Jetstream: [[spoiler:Vanity erased her memories and thus love for Stonewing after his "death", then went insane following Big Macintosh's death and put in an asylum]].
** Vanity: [[spoiler:Tried to hold the team together but quit after Jetstream's mental breakdown. Killed by his brother Blueblood for sleeping with Rarity]].
** Echo: [[spoiler:Considers himself a DirtyCoward for standing by and doing nothing as his team fell apart. He eventually was employed by Goldenblood but his soul was attached to EC-1101 to protect it from misuse. Echo became the Dealer and betrayed Blackjack to Cognitum to get back his body.]]
* Chapter 71. The whole thing is pretty gloomy, with themes of uncertainty and nopony knowing if the day fighting the Harbingers will be their last. It was clear something terrible was just on the horizon, which just makes the ending so much worse. [[spoiler:In accordance with the [[AnyoneCanDie Anypony Can Die]] theme, the ending has Glory stay to keep a rocket functional so that Blackjack can stop Cognitum from activating Project Horizons, while the both of them knowing the Legate had launched a Balefire missile with no way to stop it. Glory stays to ensure Blackjack has a chance. If the Balefire didn't kill her, the enemy shrapnel left her bleeding to death. She'd been with us since nearly the beginning, suffering through so much... But now, Glory is dead.]]
* Chapter 74. [[spoiler: Echo is devoured by mechasprites, P-21 is ImpaledWithExtremePrejudice and has to be left behind in the collapsing Lunar Astrostable. Then a page later, Rampage is shown unable to leave too, forced to hold up a mountain of metal or P-21 dies. The terminal P-21 is trying to use causes the whole place to explode, Scotch Tape offers to stay behind so Blackjack can escape, then Rampage pulls a HeroicSacrifice to get her friends to the escape rocket whilst being directly exposed to the vacuum of space and is left to wander on the Moon's surface. Blackjack plays the Johnny Cash song "Hurt", remembering her friends and wanting to stay together with them.]]