Okay, so this story isn't getting anywhere mostly due to a lot of real life problems, but I'd like to finish things rather than leave things hanging. The story was originally supposed to be very comedic/buddy cop style plot as some people have noticed with Marvel-ish Herc as a Saber class and Zelretch shenanigans
1. The Herc/Arturia swap and personality differences would have been built up to them being drawn from parallel/alternate Throne(s) of Heroes because multiverse theory and Kaleidoscope. With Herc coming from a world where he died much earlier than he did in our world in an act of defiance against the gods (involving the pillaging of their treasured weapons) to save the humans of his reality from tyranny (picture God of War's Kratos), never truly ascending to godhood, this also keeps him from accessing his FSN level of brute strength while at the same time giving him access to his repertoire of skills honed over the years. Arturia on the other hand, comes from a world where she had been driven mad by Lancelot's betrayal and the eventual fallout and the subsequent loss of Avalon causing her to fake her own death and take on the mantle of the Black Knight (Saber Alter) and sabotage Camelot unbeknownst to the other Knights of the Round Table, culminating with most of their deaths and Mordred putting up a valiant effort, shattering the Black Knight's helm with a a fatal strike, but the reveal of the knight's true face caused him to hesitate long enough for a fatal counter from his own father, Arturia would soon after fall from her wounds sustained in battle, Avalon's healing powers revoked because she had lost favor with the fae.
2. The SakuRider arc would have been concluded with Rider being Command Seal-ordered by Shinji to kill Sakura out of a mix of frustration and some more twisted Matou magecraft involving cannibalizing people for their circuits but both purple-haired women still have their proper Master-Servant sense sharing and know that Sakura's corrupted Grail form would defend her from the attempt and are forced to accept it, this event would have triggered a self-defense mechanism (which Shinji has no knowledge of), temporarily unleashing (semi)Dark!Sakura and purging herself of the worms by forcing the magic inherent in Rider's gaze on herself to petrify them (her immense prana made her immune to the Servants powers, but the worms weren't), slowly starving the nightmarish creatures to death. Dark!Sakura is then forced to tentacle-absorb Rider in order to overcome the Servant's orders and deciding to recycle some of the Gorgon's attributes for herself (a means of compensating for the massive organ damage she had just undergone with the mass vermicide), resulting in an appearance not unlike her Fate/Extra incarnation with enhanced strength and a (deliberate;y) watered-down version of Rider's Mystic Eyes.
3. Shiki and company arrive by train, followed by Akiha (who traveled by chopper because she travels in style) reach Fuyuki, all would then check in the newly rebuilt Hyatt hotel (as guests for the grand re-opening) right after meeting Rin. Behind the scenes, Ciel meets up with Kirei to check on the proceedings of the War, the priest tells her that everything is under control if not for the unwelcome interference of vampires. Ciel groans at having to work during her off-time, but promises to make some calls back to the Vatican for confirmation before leaving the Church. Gilgamesh comments on her impressive magical ability 'for a mongrel of this day and age.'
4. Rin takes the Miyaki crew around to comedic effect because she has absolutely no idea where anything is (she's familiar with the layout of the city, but never bothered to go out for leisure) causing Archer to take over for tour guide duty, ending with a look at the temple and a surprisingly dedicated Sasaki Koujiro cosplayer that had become something of a tourist attraction in the past few days. Arcueid is intrigued by the 'cosplayer's' nodachi, cuts herself by accident while touching it, leaving a trickle of blood on the blade. Kojirou sheathes the sword and apologizes for not warning her of its authenticity while a scheming Caster smiles from within the confines of the temple.
5. After splitting up with the group, Archer asks Rin if she knows who Arcueid really is and she casually replies that it's probably a distant descendant of the Kaleidoscope, only called a grandchild so the old man won't be reminded of his age. Archer is mortified at the fact that his Master was unwittingly in the company of an assassin, demi-human, Burial Agent, and True Ancestor, but keeps quiet for his Master's sanity. EMIYA instead notes how completely different this Grail War is compared to the one he participated in as a Master and wonders where it's all going to lead and what choices his foolish younger self will make. His thoughts turn to Sakura who has just been discharged from the hospital, but hasn't returned to the Matou estate, and Zoken who no longer has any pawns left in the War.
6. Meanwhile, Waver and Lorelei realize that both of them 'ain't got time for this shit' when word had spread among the instructors of the Association that the True Ancestor is now in Fuyuki and subsequently barge into Zelretch's office demanding an explanation, only to stumble into another dimension. Said dimension is populated solely by parallel Kaleidoscopes and oddly enough, some very frustrated/terrified Wavers (think Rick & Morty only with Magecraft in place of science) before being banished back to the office with a snoring Schweinorg on his table. Both Magi try to piece together what they just saw, but agree to figure it out once outside the office of the man who muddles with the laws of reality. Leaving the Kaleidoscope's office post-uninvited entry triggers a defensive spell that erases recent memories, particularly those that took place in the premises of Zelretch's office. The old man wakes up and grumbles "That wasn't part of the plan."
7. Back to Fuyuki, Shirou wonders if Sakura is alright, with Herc making a crass comment that she'd feel better after a few rounds of 'you know what I'm talking about *wink wink nudge nudge*' (but Shirou doesn't because he's dense and that's in character for him), and decides to visit the Matou estate on the way to work after school. Herc!Saber spends the day doing various 'Labors' for the citizens and stumbles upon an exhausted Shiki while looking for some cookware. Shiki asks the much larger man why he goes to the trouble of doing things that people could do for themselves and the Heroic Spirit answers that it's more than just the task at hand, but the knowledge that a helping hand is nearby. Shirou bumps into the two on his way to work and catches part of Herc's speech and quietly moves on, but not before catching a glimpse of what looks like a weapon protruding from Tohno's pocket.
8. Shirou comes running to the Matou estate, only to find it in flames and recklessly rushes into the blaze, heading straight for Sakura's room, but finding nothing in the smoke. Reaching Shinji's room reveals a bloody hand that was once attached to his friend. Zoken is nowhere to be seen and Shirou can't escape, forcing the young Magus to use a Command Seal to call forth Herc as the flames draw near.
9. Herc and Shiki are looking for the rest of the Miyaki crew as both fighters sense an air of foreboding around the city, they split up and not soon after the Command Seal kicks in and ports Herc to Shirou's location. The Lion of Olympus manages to safely get his now unconscious Master out of the estate, not noticing a stray worm having sequestered itself on the boy's shoe or the Einzbern-made alchemical construct watching over him.
10. At Illya's castle, one of the albino maids commend Shirou's guts in taking on one of the oldest and most powerful magi in Fuyuki head on, not knowing that Shirou had nothing to do with the fire or the destruction of generations of Matou research. Illya then makes plans to attack the Emiya estate, creating several familiars for the occasion as well as authorizing the use of her maids' full powers
11. Sakura hides away for the night at one of the old Tohsaka properties that Rin and Kirei have left all but abandoned. The purple-haired girl has her first good night's sleep since being turned over to the Matou. However, an invisible ward triggers, alarming Kirei Kotomine that someone has entered, but the magecraft based defenses fail to trigger as they recognize Sakura as a Tohsaka. This alerts Kirei that something must have happened to Zouken as he looks at the fire coming from the direction of the Matou estate. Sakura discovers a door locked by both magic and conventional, but she can sense something sinister on the other side and decides to leave it alone and flees the city immediately.
12. Meanwhile, in Ryudou Temple, Caster sends several skeletons to salvage anything usable from the Matou compound. Assassin is left to guard the gate with a crude bone sword as his summoner had taken to examining the blood of the tourist that cut herself on his blade. Kuzuki keeps to himself, but internally notes that he sensed a presence similar to himself earlier in the city.
13. Ciel goes on patrol and decides to investigate the charred remains of the Matou estate and engages Casters skeleton army. From the distance, Lancer stands impatiently, having been ordered by his Master to keep tabs on the Burial Agency's operative.
14. The next day, Shirou and Shiki bond over their shared passion for cooking, making breakfast for the whole group. While cooking, Shiki leaves his knife on top of his backpack, which doesn't escape Shirou's notice. Shirou is concerned that Sakura still hasn't shown up and it is at this point that Archer materializes and reports to Rin that Sakura is still within city limits. The Servant's presence causes a bleed-out effect with his present day self, triggering Shirou to fully analyze the bloody history of the Nanaya family heirloom, knocking him out instantly.
15. *Insert Filler Arc with the Tsukihime cast*
16. Back at London, Waver and Lorelei realize that they had been attempting to make contact with the Wizard Marshall for over a week when Waver's secretary points out that the other professors have been waiting for their report. This results in the pair attempting to formulate a method to enter Zelretch's office without triggering the mind-wiping ward. This has the unintended effect of several rumors about a secret relationship between the 'Queen' and the former Master pop up from both the student body as well as the faculty. The Kaleidoscope catalogues every rumor in one of his inventions for his entertainment, laughing the entire time.
17. Caster is given an anonymous tip that there are several interesting 'ingredients' spread throughout Japan that would be useful for both her research as well as for affecting the outcome of the War. At the Servant's request, Kuzuki takes a few of Caster's animal familiars and some enchanted combat gear to procure them...At Miyaki City.
18. Shirou's been out cold for approximately 2 days when Akiha is informed that the Tohno manor has been broken into, Hisui has been kidnapped and Kohaku was injured, but alive. She and Shiki immediately book it for their home in order to investigate while Ciel remains in Fuyuki to aid in the potential vampire suppression and Arcuied cryptically informs Rin that she cannot leave until a certain Wizard Marshall contacts them both.
19. Archer begins searching for clues as to Sakura's whereabouts when he encounters Lancer, currently on an errand for Kotomine. Both Servants clash until their duel is interrupted by a few stray ghouls. Both Servants dispatch the interlopers and decide on an uneasy truce and fall back. As they leave, a small number of worms crawl out of the fallen undead towards the bloodstains the Servants left behind.
20. Sakura is in an unknown forest when she happens upon a small cabin inhabited by none other than Kishima Kouma. They immediately understand that the other is a similar inhuman existence, however, the Crimson Red Vermilion, now a hermit of sorts, takes no action and merely observes the high schooler. Deeming the girl to be no immediate threat, Kouma offers her a place to rest for the evening as he goes out to hunt deer for dinner. Eventually, Sakura asks for Kouma to train her to control both her part-Servant abilities as well as any residual programming that Zouken may have left behind. The stoic survivor of the Kishima clan agrees, only if Sakura helps him find someone...His son.
21. Shirou awakens from his short-lived coma, only to discover that most of his guests had already left and that Herc was practicing his swordsmanship in the dojo. The redhead recalls an earlier dream where Herc wielded a considerable arsenal, most of which weren't even associated with his legend on this reality. Both men decide to spar as a way to get Shirou in shape for the coming battle, as well as better familiarizing himself with Herc's fighting style. Only to end with the teen being caught by a surprise piledriver, teaching Shirou the value of thinking outside the box.
22. Kuzuki and the familiars are on their way back from Miyaki, the ashes of SHIKI Tohno in tow. However, their escape route happens to pass by the forest that Kishima Kouma resides in, and the oni-blooded man is able to sense faint power emanating from the remains of the firstborn Tohno and unwilling to ignore the possibility that it is his offspring, begins his advance towards the former assassin. Meanwhile, Sakura had been sent on a training exercise deeper into the forest in order to fine tune her control over her abilities. The Crimson Red Vermilion meets face to face with the educator and surmises that it is a Tohno and not a Kishima in the urn, still bound by the blood oath of his ancestors to the Tohno clan, he does battle with the assassin in a battle of overwhelming might vs. peerless skill.
23. The council of the Kaleidoscope announce the unfortunate passing of one (non-vampire) member due to old age and hold his Magic Crest up for lottery. Eventually it ends in the hands of Fate:Distortion's Zelretch who remarks that while morbid, it accelerates his plans as he already knows exactly what to do with it, before returning to his office.
24. Shiki and Akiha arrive in Miyaki and are forced to combat a horde of unusually powerful skeletons. The enemies seem endless in number until Shiki uses his Mystic Eyes to trace their point of origin to a 'generator' of sorts. It's when the prodigious assassin comes in contact with the cursed artifact does he realize that it's utilizing blood from Arcuied. Much later, Kohaku elaborates that only recently drawn blood could have been utilized in its construction and it dawns on Akiha that whoever is responsible for the attack has some relation to the Sasaki Kojiro 'cosplayer' in Fuyuki.
25. Illya decides to gun for Shirou, still under the impression that he's responsible for killing Zouken, and thus, the biggest threat to her in the war. Sella and Leysritt likewise prepare for battle and equip themselves with recently delivered 'parts' straight from Einzbern manor. Arturia is unusually behaved as all the preparation is going on, however, the Servant detects a faint hint of familiar-type magecraft coming from just outside the manor and the wards. Cut to Gilgamesh, seething with anger at what has become of his 'Saber'.
26. Sakura practices the kata that Kouma had instructed her with when she is beset upon by more of Caster's skeletons. However, their lack of humanity gives her little reason to restrain herself and she makes quick work of them unarmed. Realizing that there could be more in the forest, she frantically searches for Kishima Kouma. The purple-haired girl arrives to the site of the grueling duel between assassin and monster. Her presence momentarily distracts her former teacher enough for Kouma to deal a crippling blow. Kuzuki is saved from a fatal follow-up by one of Caster's bone soldiers and is forced to drop SHIKI's remains in order to escape, only managing to take with them some of the late Tohno's personal belongings. After the enemy retreat, Kouma goes into a bloodrage due to his injuries and Sakura is forced to defend herself.
27. Archer continues his investigation on Sakura when he runs into Ciel, herself looking into the spike of the unusual 'ghoul' population in Fuyuki. The Burial Agent is surprised that the silver-haired Servant already knows of her and EMIYA suggest that they each go their separate ways. This idea is dashed when corpses come out of the woodwork, enforcing a temporary team-up between the two. It is when Archer catches sight of the trademark Matou worm does he realize where the ghouls are coming from.
28. Flashback to before Shinji Command Seals Rider into killing Sakura. The blue-haired fool breaks into the Matou basement and releases several prisoners held there by Zouken to wreak havoc...Including an almost Dead Apostle-level Tohsaka ancestor and former friend from when Zouken was more 'human', unshackled and thirsting for blood, he kills Shinji and sets the estate ablaze, including the workshop where Zouken had been cultivating experimental 'vampire' worms for later use on himself.
*The two truly were comrades and the Tohsaka ancestor was the one who convinced Zouken to move to Japan and start his line in Fuyuki. His imprisonment was a willing one, having been tasked by Zelretch into killing a middle-rank vampire and succeeding at the cost of his humanity, he had asked the Matou head to keep him away from his own family before his instincts take over. However, as the years went on and the man named Zouken Matou withered into his current single-minded self, he started using his old friend as a means to further his research.
29. A worm-ghoul hybrid Shinji attacks the Emiya household with several weaker ghouls in tow. Herc is able to fight many of them off, but Shirou is infected by several worms. Right before passing out, Shirou manages to project the Sword of Peleus (Look into Marvel) from his dream and throws it at Herc who proceeds to mow down the horde, forcing Shinji to escape. As the dust settles, it's clear that Shirou's injuries are far graver than they appear.
30. The Fujimura clan note similar happenings involving the ghouls throughout Fuyuki and Taiga notices Herc jumping rooftop to rooftop with an unconscious Shirou in hand. Raiga stops her from leaving and orders the other men out of his office. It is then that he reveals an old stack of documents that Kiritsugu left behind in case 'weird shit happens', including the disclosure of magecraft, the extent that magi go to keep its secrecy and some of his enchanted weapons caches located throughout the city. When confronted on how unbelievable it sounds by his granddaughter, Raiga laughs it off saying that he'd known since forever and that the Fujimura and Tohsaka clans were actually closely involved with running the city, one clan handling the mundane and the other, the supernatural. The grandfather then pulls out an ornate box with a seemingly innocuous katana inside and hands it to his granddaughter, saying that it's her early inheritance given the current situation, he then tells her to place her 'lucky charm' around the sword, which unlocks its sealed power, a weapon only for the heir of the Fujimura, forged by Tozaki (who gambled his services and one of his bones to an ancestor) and enchanted by a Tohsaka (who also gambled his services to the same ancestor on the same game).
*And if anyone's curious, yes, the Fujimura ancestor did in fact rig the and because neither magi nor demon-blooded blacksmith considered that a thug would cheat in a game.
*The Fujimura katana is normally equal to an E-Rank Noble Phantasm, but gets promoted to a D- because of a double homefield advantage, being in Japan as well as Fujimura controlled territory
AN: And that's about 30 Chapters worth of summarized plot, the rest will come hopefully by April.