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.
Consequently, P-21's attempted suicide in Chapter 25.
Blackjack's reunion with Glory in chapter 25. Glory is initially livid with her over her suicide attempt but gradually breaks down and confesses that, without Blackjack, she had nothing left to live for.
Blackjack's tearful reconciliation with P-21 at the end of Chapter 33, and subsequently, her death.
Chapter 43. All of it. Everything from Blackjack's heartbreaking refusal to believe that her friends don't exist outside of her mind to her finally reaching some level of closure with her mom to the abandoned Happyhorn computer slowly trying to comprehend that it can't ever fix her.
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 Heroic Sacrifice and destroys herself to restore the memories of her sisters. Psalm is resurrected as a result, but she is not Lacunae.
Big Mactinosh: Gunned down by Psalm in an attempt to assassinate Princess Celestia, and his death was made to look like a Heroic Sacrifice.
Applesnack: Reassigned to guard Zebratown, became the first Steel Ranger, murdered Zecora, broke up with Applejack, and then became a ghoul.
Twist: 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: Went from a devoted follower of Luna driven by faith to a self-loathing Cold Sniper. 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: Manipulated by Brass into raping Twist, sent to Hightower Prison, grew to hate all mares, and eventually transformed into Deus through Project Steelpony.
Stonewing: His death was faked by Sanguine so he could be used for Project Chimera and transformed into Gorgon.
Jetstream: 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: Tried to hold the team together but quit after Jetstream's mental breakdown. Killed by his brother Blueblood for sleeping with Rarity.
Echo: Considers himself a Dirty Coward 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. In accordance with the 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.