Fuyuki: Lev Lainur, a member of Chaldea's staff whom you had met earlier, reveals himself to be a servant of the Big Bad, and promptly kills off Chaldea's director, Olga Marie Animusphere, in one of the cruelest fashions the Nasuverse has to offer, after the protagonist had just spent the entire Singularity getting to know her and seeing through her rough exterior.
Septem: Lev reveals that his full name is Lev Lainur Flauros, then transforms into an Eldritch Abomination. Cue the game's first battle against a Demon God Pillar.
London:
The Big Bad behind the Singularity is none other than Zolgen Makiri, aka Zouken Matou. Who'd have thought he'd have an express role in the Big Bad's plot?
The Singularity then ends with a confrontation with the Greater-Scope Villain: King Solomon. He forces you to fight four Demon God Pillars at once, and then wipes out nearly all of your allies after the battle anyway and declares that compared to him, you are less consequential than piss.
E Pluribus Unum: At the end, after you've returned to Chaldea HQ, Mash collapses suddenly. It turns out that she has a shortened lifespan and won't live to see past 18.
Camelot: At the very end, Dr. Roman manages to figure out that Bedivere, whom you've fought alongside for most of the Singularity, isn't a Servant after all, but just a human. We then learn that this Bedivere never returned Excalibur to the Lady of the Lake, and had spent the past 1500 years trying to return it to its rightful owner.
Babylonia:
Upon returning to Uruk after winning Quetzalcoatl over to their side, the protagonist is greeted by a tearful Siduri, who informs them that Gilgamesh is dead. One of the greatest heroes in human culture, and he's died of overwork. Fortunately, the protagonist is able to bring him Back from the Dead by taking a trip into The Underworld...
Toward the end, in the midst of their titanic struggle against Tiamat, the heroes force her into the Underworld...and who should meet them but Merlin, who was killed earlier in the Singularity. But that's not all — the old man whom you helped earlier in the Singularity reveals himself to be none other than the first Hassan-i-Sabbah. Without hesitation, he sacrifices his Grand vessel and attacks Tiamat, rendering her able to be killed.
Solomon:
It turns out that Dr. Roman is the real King Solomon, having taken on a human form after winning the Fuyuki Holy Grail War a decade earlier. He then performs a Heroic Sacrifice to bring Goetia's master plan crashing down and render him vulnerable to the protagonist.
Salem: The introduction of the Foreigner class and how they bring the Lovecraftian Outer Gods into the game.
Arc 2
Prologue/December 26, 201X: Chaldea is shut down thanks to being bought out, and all of the Servants are sent back to the Throne of Heroes.
Anastasia: Near the end it's revealed that if the party destroys the Trees of Emptiness to make the Lostbelt disappear, rather than having it go back into its proper order like with the singularities. It gets wiped out completely. Meaning that Chaldea has to wipe out everything living in the Lostbelts if they want to have a chance to undo the damage the Foreign God did.
SIN: When the party backs Hinako in a corner with her heavily wounded she ends up devouring the Prince of Lanling at his request, revealing that not only is she the wife of Xiang Yu, Yu Mei-ren. But that the reason she's lived this long is do to being a True Ancestor.
Yugakshetra
Rather than simply being a god or godlike being like the previous Lostbelt Kings, God Arjuna is a being composed of the entire Hindu Pantheon making him far more powerful then anything faced up until this point
When backed against the corner Daybit comes in to save the party and Pepe with his servant while not much is revealed about either, the one thing that’s known for sure is that Daybit somehow made a contract with a Grand Servant.
Atlantis:
The Olympian Gods were originally Humongous Mecha who in this timeline never bothered to default to human forms thanks to not having their physical bodies destroyed. Thanks to this they are immensely powerful to the point that Artemis can fire off beams on par with Anti-World Noble Phantasms.
At one point Chaldea faces off against Wodime personally without any of his servants..... and he absolutely destroys the party with magecraft powerful enough to allow him to stand on par with the gods.
After Wodime defeats the party, The Man From Chaldea finally reveals himself to the party in person to convince Wodime to give the heroes a second chance like the Crypters did. During this it's shown that while he does look like Romani, it's heavily implied that Goetia simply stole his body after Solomon's soul left it.
After being absent for the first half of the Lostbelt storyline. A Grand Servant arrives in the form of the Grand Archer, who is Orion of all people utilizing the full power of Artemis's blessings.
Olympus
In order to even the playing field against the remaining Olympians, Mash ends up getting a replica of The Black Barrel
When interacting with Tamamo Vitch, Sherlock ends up revealing that she gives off signals that identify her as a Beast, which Vitch then uses as an excuse to attack the party in her immature Beast form.
Wodime's plan is finally revealed. He plans to betray the Foreign God by having Atlas stop their decent to earth and use the power of a fully grown Tree of Emptiness to ascend every human on Earth into full on gods.
At the end of the story the Foreign God finally reveals themselves, and not only are they Beast VII but they also inexplicably have the body of Olga Marie.
Avalon La Fae
Caster Cu is revealed to be a pseudo-servant of Odin from Norse Mythology.
The British "Lostbelt" is now actually a Lostworld (a.k.a. a timeline that ran completely parallel comparable to Proper Human History).
Chaldea was unable to defeat Morgan in battle as the “Morgan” they defeated in battle was just a clone of her.
Oberon is actually Vortigern from the Arthurian Legend, and he was brainwashed into thinking he was Oberon. He's also revealed to be part of a brand new class at release called the Pretender class.
Traum: The Foreign God's first apostle was none other than Holmes himself. Upon remembering this, he also willingly killed himself so he wouldn't become a threat to Chaldea.
Nahui Mictlān:
Your main ally for this chapter? It's U-Olga Marie out of all people.
After breaking the first break bar of ORT at the end of Part One, it ends up gaining nine break bars, and a total of 3,591,250,000 HP.
After seemingly being defeated, ORT then emulates a Lost History that the Throne of Heroes will accept and manifests itself as a Grand Foreigner capable of resummoning itself as long as a part of it still exists; It takes the Lostbelt King pulling a Taking You with Me to put ORT down for good.
U-Olga Marie is not the real foreign god; it's Marisbury/CHALDEAS.
Arc 2.5
Id: Nearly every Avenger is forced to leave Chaldea to head to Antarctica ahead of them because the protagonist's belief in salvation cannot be reconciled with the Avenger class's concept of destruction.
