Fate/EXTRA/WMG

The 6th Master wasn't trying to directly kill the main character before the final fight.
Numerous times near the beginning of the week, it's commented on how "an incredible urge to kill" was approaching the character, but then would stop and go away. It's implied that this is  setting up an attack but then not able to go through with it. While a Berserker would make sense; the exact same dialogue is for Lancer's path as well. What was happening was that the 6th Master was fighting ; which is why his pin was in the fountain. It was a combination of this and dealing with conflicting emotions in fighting the main character that lead to the events of the 6th week.

All NPCs are sentient.
They sometimes act dumb; but they all show signs of self-intelligence; usually just in front of the main character; who doesn't count if they slip.

Moon Cell is "The Matrix" for everyone on Earth.
As stated, the Grail War is a very small subroutine. In the main function of the program (which nobody has access to), exists a virtual copy of Earth that uses Earth's lost prana to function on its own.
 * Nobody is deleted when they lose a Colosseum match. The Moon Cell records; it doesn't delete. It just moves their data to a different folder. (non-accessible.) However, their bodies on Physical Earth still die.  They are likely merged with the copied record of themselves. (No reason in having two.)
 * Archer just thinks they all get reprogrammed; but Taiga does say; if you do all her requests; that she's "going home."
 * It's mentioned, however, that Taiga and Issei (and similar NPCs, presumably) are different from the standard NPCs which are randomly chosen to fill the roles needed during the War. It's possible that these special NPCs are in fact retained with either their memories of the Wars or at least with knowledge that they were there, and just re-used when the next tournament comes around.

Moon Cell is an attempt to escape Program Number Six.
When "the disaster" occurred; it took the opportunity to absorb all the prana from the world to begin "animating" its backup records. It's copying the existence of Earth so that when the end comes, a type of Earth will still exist for backup purposes.
 * Unlike Dust of Osirus, it's more than just a record; it's interactive. After Program Six hits; someone will use the Moon Cell's function to "reboot" Earth.. This is the original function that the Grail War created a back door into.
 * The Main Character

Only a special quality can summon a true Divine Servant.
Much like how only another Servant can summon a fictional Servant; an  can summon the Divine as their Servants because they share a quality with them; that of   Note; this is a funny condition in the Nasuverse that has nothing to do with not existing. (Example: The Demons in DDD).
 * Which is why
 * This is impossible/highly improbable in the main universe because of the unique nature of Moon Cell.

This particular Archer EMIYA was adopted by a Kiritsugu still in Magus Killer mode.
According to Extra, The Magic Goes Away during the 1970s; Fate/stay night happened in the 90s, placing Fate/Zero in the eighties at the latest since Stay/Night occurred ten years after the previous Grail War. It's not implausible that Kiritsgusu would have been a 'hitman' regardless, he just shifted his focus to the Western European Plutocracy that would have taken the place of magi as the threat oppressing/misusing Mankind. Prior to becoming Archer, was not only affected by overuse of thaumaturgy, his hair white and his eyes graying, but is depicted with a scoped sniper rifle not unlike those used by Kiritsugu in Fate/Zero. With a more hostile world climate than that of the 'original' timeline, the prevalence of orphans would not be unlikely: Dialogue about the real world indicate it was in a state of open war thirty years prior, most tellingly in Twice's flashbacks and Alice's mention about men with tanks and guns and metal helmets. The-boy-would-be-Shirou was orphaned and adopted by Kiritsugu as before, only instead of it being a result of the Fuyuki Fire it was the kind of instability and conflict you'd expect from a world at war.

Unlike the original timeline, Kiritsugu didn't have the option of teaching Shirou 'useless' lessons or shielding Shirou from his past: Originally Kiritsugu intentionally failed to teach Shirou competitively and hid his past, allowing Shirou to grow up with an idealized version of "heroes." In this timeline, with war very real and threats to the kid tagging along with Kiritsugu a constant, Kiritsugu began actively training Shirou for combat: Not only through what magic could still be used but in straight-up mundane tactics as well, accounting for the depicted rifle and possibly the reference Archer makes about cross-hairs and underhanded tactics (not unlike Kiritsugu's original pragmatic mindset) while bantering with Robin Hood in the elevator. Kiritsugu died but Shirou carried on with his ideals, not just metaphorically like the original Shirou but literally carrying on his mission against the Plutocracy; the similarities between the pre-Archer artwork and may indicate that they were both indeed part of the rebellion, though it's likely Kiritsugu would have worked with such a group at least nominally since their aims ran parallel. The difference in portrayed daylight - Shirou in daylight with the sun beginning to set, Rin in the evening - could parallel the difference in activity: Rin doesn't look old enough to have been around before or early in the thirty years of peace, so the increase in 'night' portrays the Harway lockdown on their opposition that's occurred since then.

Without the luxury of peace and normality experienced by FSN Shirou, Fate/Extra Shirou set off down the trail that Kiritsugu had blazed, a path which ended much like what Kiritsugu might have experienced had he continued as the Mage Killer: Following his ideals without factoring in human emotion eventually isolated Shirou from his loved ones, becoming the embodiment of impartial Justice that FSN Shirou avoided by placing his humanity first. In another similarity to (at least one alternate version of) the original Shirou, Extra's Archer became a Servant despite his lack of legend, agreeing to serve the Moon Cell not unlike how Fate/Stay Night's Archer became a Counter Guardian.

Li'l Ronnie suffered a massive psychotic break as a result of Post Traumatic Stress Disorder.
It's been established that until thirty years ago the world was at war, and in more recent years there's been a considerable amount of violence; Twice says as much when he mentions trying to "save" the world. Ronnie appears to be older than the average Master, at least old enough to have had a child, so it's possible she lives in an area devastated by war. Starvation is a very real threat in war-torn areas, or areas economically devastated by a powerhouse such as the Harways; with no other food at hand, Ronnie killed and ate her pet bird in order to survive, possibly rationalizing that a broken wing might as well have been death for something meant to fly. The trauma of living as she did had already worn away at her sanity, and being forced to eat something she held dear caused her to equate the act of devouring with love; indeed, some view the act of eating and "becoming one" with your meal to be the utmost intimacy.

It's also possible those around her died of various causes and to 'keep them with her' she ate them, ensuring her survival but digging herself deeper into madness. Ronnie mentions that "now, everybody is gone," and since it's unlikely she managed to depopulate an entire community/ect on her own it may mean that where she lived has been depopulated through the effects of war; she says she only wants to eat 'what she loves,' which prevents her from just eating other people like a "normal" cannibal would. Her loved ones are all dead and her psychosis prevents her from wanting to eat anyone she doesn't care about, so she plans on asking the Holy Grail to 'make everyone likable and her friend,' ensuring that she can love - and therefore eat - anyone.

The city in which the terrorist attack occurred and where Twice and the MC died, is Fuyuki City.
Because it's mentioned to be "a city in the Far East" (i.e. Japan) and is thematic with the series, not to mention the presence of Archer EMIYA. Talk about a Doomed Hometown.

Twice Pieceman was the sole surgeon capable of performing the MC's operation.
When he died in the same attack that took the life of his would-be patient, the latter was recovered before they died; but, with the only qualified specialist dead, cryosleep became the only other option. Twice was, after all, noted for his advances in neurosurgery, which sounds like the kind of guy who might be the only one capable of performing advanced brain surgery to counter a neurological disease, and of course he was around in the same part of the century that the MC originates from. Also, for the Dramatic Irony.

The comic book you get for trading the Student Council Badge during Taiga's Week Six quest...
... belonged to the male Master in front of the school who was always talking about comics, and asked you to choose a side in the Comic Book vs. Manga debate. The NPC you get the comic from says it was supposed to have been deleted with the Master who owned it and the comic-fan Master is gone beginning with that week, presumably having lost his match and been erased.

Shiki Tohno will have a cameo in Fate/EXTRA CCC
...because if, this makes sense. Also, Shiki might ask if he's looking for  as an inverse of what happened in Fate/EXTRA.