In Chapter 5, Sigurd is escorted to the capital of Grannvale, ostensibly to be cleared of all treason charges, but Arvis reveals that he has married Sigurd's kidnapped and amnesiac wife Deirdre, and orders his execution. Cue Total Party Kill and The Hero Dies, end of part 1, begin part 2 starring his son Seliph.
At the end of Chapter 27, an Ice Dragon appears out of nowhere and Eliwood's newly-acquired Infinity +1 Sword moves his body on its own to kill it, only for Nergal to show up and reveal this Ice Dragon was Ninian.
Chapter 14, Eirika's Route: Joshua is the prince of Jehanna, and his mother dies.
Chapter 14, Ephraim's Route: Emperor Vigarde isn't merely Not Himself, he was Dead All Along, and the true mastermind of the war is Lyon.
Chapter 17, both routes: Lyon is possessed by the Demon King.
Chapter 18, Ephraim's Route (moreso if the player has already completed Eirika's): Unlike on Eirika's route, where Lyon is wholly innocent and it's a bog-standard Demonic Possession plot, here Lyon reveals that he let the Demon King possess him willingly, and fought off the possession, meaning he was in control of his actions all along. He wants to use the Demon King's power to help the world. This resulted in Lyon having his darkest emotions such as his jealousy of Ephraim, love of Eirika, and viewing himself as a weak ruler manipulated by Fomortiis, and thus turning him into an indirect pawn of the Demon King.
The end of Chapter 19, where Volke is revealed to have been hired by Ike's father all along, and reveals the real story of what happened to Ike's mother: Ike's father killed her when he accidentally touched Lehran's Medallion and went insane, afterwards he cut his own arm so he could never wield a sword again. Volke's true identity is an assassin hired by Ike's father to kill him if he ever went mad again.
The end of Part 3 and the beginning of Part 4, where the goddess sealed inside the medallion is released, most of the world's population is turned to stone and The Reveal that the sealed goddess was actually Good All Along and the real enemy is the goddess everyone thought was the good one. Cue plot shift from continent-spanning war to fighting a god.
Chapter 9: Phila, the commander of Ylisse's Pegasus knights, is killed by the Risen Archers alongside her troops in an attempt to rescue Emmeryn from execution, and as a result, Robin's rescue plan fails. Emmeryn thus sacrifices her life to save Chrom from having to trade the Fire Emblem to Plegia to secure her release, leaving so many people devastated, including her brother and her sister.
Chapter 10 counts as even more of one, as the Plegians who saw Emmeryn's sacrifice don't want to fight anymore, and even their general, Mustafa, wants to try to solve this peacefully, knowing full well it's far too late for that. Said general must fight anyways for his family, and his soldiers now only fight for him, and not their king. Oh, and you can't recruit him, even though he's one of the more sympathetic bosses in the series, you have to kill him to complete the Chapter. Couple that scenario with music like this and this right at the start and you have Grade-A Wham Episode material.
Chapter 13 almost seems to be trying to set some kind of record for most Reveals dropped at once. Plegia has a hierophant who looks identical to the Avatar and has the same name, and Validar reveals himself as the Avatar's father and that the Avatar was born to be a vessel for the Fell Dragon Grima. At the chapter's end, "Marth" reveals herself to be Lucina, Chrom's Kid from the Future, who has travelled back in time from a Bad Future where Grima was revived and wiped out humanity, in order to change history. The sudden reveal of Time Travel elements drastically changes the rest of the story and even gameplay.
Chapter 21: The Avatar was the cause of the Bad Future, and Lucina plans to kill them to Set Right What Once Went Wrong, but is talked out of it by Chrom (or is unable to go through with it if the Avatar is her mother or husband).
Chapter 23: Validar isn't as good a schemer as he thought, as it turns out Basilio faked his death earlier in the game and replaced one of the gemstones in the Fire Emblem with a fake, preventing him from resurrecting Grima. BUT at the end of the chapter the hierophant appears again and is revealed to be the Avatar from the Bad Future timeline possessed by Grima, and completes the ritual himself.
All routes, Chapter 5: Mikoto is killed using the sword Corrin brought to Hoshido, kickstarting the war and Corrin's big choice.
Birthright, Chapter 17: Flora was leading the army into a trap all along and kills herself after being defeated.
Birthright, Chapter 26: Elise takes the blow meant for Corrin and dies, causing Xander to pull a Suicide by Cop.
Conquest Chapter 15: Garon is Dead All Along and the Garon we know is a monster.
Conquest Chapter 25: Ryoma commits seppuku rather than see Corrin die for disobeying Garon.
Conquest Chapter 27: The thought-to-be-dead Takumi attacks Corrin, hell-bent on destroying him/her and Nohr. Azura realizes whatever was behind Garon the monster is keeping Takumi's body alive.
Revelation Chapter 7: The hidden kingdom of Valla is behind the whole war, and is ruled by the Silent Dragon Anankos.
Revelation Chapter 22: The mysterious woman working for Anankos is Azura's mother Arete, trapped under Anankos's control.
Revelation Chapter 24: Anankos has resurrected and is now controlling Mikoto as well.
Hidden Truths DLC: Anankos is a Tragic Villain and Corrin's real father.
Heirs of Fate Chapter 4: The Hoshidan children and Female Kana come from a timeline where Birthright happened, and the Nohrian children and Male Kana come from a timeline where Conquest happened.
Heirs of Fate Chapter 5: Shigure, however, comes from a timeline where Revelation happened. Unfortunately, everyone but him died fighting Anankos.
In a rarity for the series, a Support Conversation manages to be one of these: Edelgard's C+ support with the Player Character. It starts innocent enough, before revealing that she was subject to brutal experimentation to awaken a Crest within her, and her other siblings were "sacrificed" for this purpose. She then reveals the results of the experiments: she bears a second Crest... the Crest of Flames, the same one the protagonist possesses. Notably, viewing this conversation is required if you want to side with her later on.
Chapter 11, the second-to-last one before the Time Skip, where the reveal of the Flame Emperor's identity throws everything into chaos. It's especially brutal on the Blue Lions route, where the Dramatic Unmask comes via a pre-rendered cutscene, and finding out his hated enemy is his childhood friend and step-sister causes Dimitri to Go Mad from the Revelation. Furthermore, on the Black Eagles route, this is the point where the story splits and you are offered a choice—join Edelgard in her war against the church or defend the church against her, Hubert, and the rest of the Empire.
The second battle of Gronder Field on the Azure Moon (Blue Lions) route becomes one when, after the battle, the younger sister of an Imperial general Byleth killed tries to assassinate Dimitri, resulting in Dimitri's Parental Substitute Rodrigue sacrificing himself to save Dimitri. This, and a heart-to-heart conversation with Byleth, helps Dimitri come to his senses and give up his quest for vengeance in order to redeem himself and liberate the Kingdom of Faerghus.
Part I of the Scarlet Blaze route ends with the Imperial army foiling an assassination attempt on Edelgard. All signs point to a mole in the palace tipping off the Knights of Seiros to her return, and the prime suspect, the former Duke Aegir (whom Edelgard deposed in the prologue to regain control of the Empire), escaped from his confinement.
Part I of the Azure Gleam route has Edelgard's initial gambit blow up spectacularly when a very irate Thales takes advantage of her loss at Arianrhod to bend her to his will and steal back control of the Adrestian Empire, right after Edelgard tells Dimitri that Thales was responsible for the Tragedy of Duscur.
Part I of the Golden Wildfire route sees the Alliance's victory against the Empire at Gronder Field get cut short when Shahid sends a massive army of Almyran soldiers to attack the border and avenge his loss from two years ago. After Claude defeats and kills Shahid, the Leicester Alliance convenes several months later and votes to disband and reform itself as a federation, with Claude as its leader and king.
The first major battle of Part II of the Golden Wildfire route has Claude abandoning his new ally Randolph to use as bait so he can kill Catherine, one of the strongest members of the Knights of Seiros. No oneis happy with Claude after this, least of all Randolph's little sister Fleche, who sics Jeralt's Mercenaries on Claude and the Leicester Federation army in the very next chapter after she learns of her brother's death.
One chapter in Part II of each route (Chapter 10 in Scarlet Blaze and Golden Wildfire, and Chapter 12 of Azure Gleam) has your enemy hiring Byleth to help stop your army in its tracks. After several lopsided beatdowns, you've finally become strong enough to turn the tables and beat them once and for all...but if you do so, you're forced to kill Jeralt, which causes Byleth to go on a Roaring Rampage of Revenge and kill a character close to your lords in retaliation.
And even if you follow a very specific strategy to avoid fighting Byleth and get them on your side, Chapter 14 ends with Arval (or the Agarthan deity Epimenides acting through Arval) hijacking your body and attempting to kill Byleth anyway, leading to a pair of missions where your army has to snap the protagonist out of their rampage, and then the three lords call a temporary ceasefire when they all get sucked into a parallel dimension and have to kill Epimenides and shadow clones of themselves and their retainers to return to their world.
In the aftermath of Chapter 10, the Fell Dragon Sombron is revived, and Veyle, the girl Alear helped out in Firene, turns out to be his daughter. They steal and corrupt the six Emblem Rings and the Draconic Time Crystal, temporarily robbing the player of the game's major mechanic and forcing Alear's army to flee southward to the Queendom of Solm as the Four Hounds give chase. It takes Ivy pulling a Heel–Face Turn and providing the army with two of Elusia's other Emblem Rings to give the heroes hope and a chance to retreat and regroup.
In Chapter 21, the heroes' army returns to Lythos Castle to meet with Veyle, whose Superpowered Evil Side has been amplified by a Mind-Control Device Zephia placed on her. Marni is killed by Zephia after attempting to destroy it, causing the normally stoic Mauvier to hit his Rage Breaking Point and defect from the Four Hounds on the spot. The heroes' victory over Evil Veyle is undone when Sombron, now with all twelve Emblem Rings in his possession, kills Alear as they block an attack meant for Veyle, and uses his newfound power to raise his homeworld of Gradlon from the sea as a springboard for seeking out other realms to conquer them. When Alear meets Veyle in the afterlife, they suggest having Veyle revive them as a Corrupted as a last-ditch effort to stop Sombron.
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