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How Fate/Prototype would end
Misaya, Sancraid, Caster's Master, Rider, Caster, Assassin, and Berserker are killed in the war. Ayaka has three Servants: Saber, Lancer (as a result of Sancraid's theft of Saber, whom Ayaka took back from him after forming a contract with Lancer), and Archer (after the skyscraper president withdraw and offer his Servant to Ayaka and provide some assistances for her in the war).

The three knight classes and Ayaka went to their final battle against Manaka, Servant Beast, and the fallen 6 Servants from the Previous War. Near the end of the battle, Ayaka went through an "Awakening" (unleashing the holy relic sealed by her father) to aid her Servants a way to eliminate the Beast, rising up the Master Rank from Princes to Seraphim, causing her sister to demote to Princes.

Manaka and the Beast, along the Servants of the Previous Grail, were finally killed, and the Grail was destroyed once and for all. Only Ayaka and the Skyscraper President were the last surviving Masters of the Grail War. The story ends with these two scenarios:

  • Scenario A (Based on Fate): They fade away after the war, returning to the Throne of Heroes (or for Saber's case, to Avalon) after Saber confessed his feelings for Ayaka.
  • Scenario B (Based on the True End of Heaven's Feel): Under some circumstances, they were able to maintain they existence after the Grail's destruction that they all decided to stay with Ayaka, and thus will begin the beautiful reverse harem triangle we all know and love.

If Fate/Prototype would ever be an Otome game, Ayaka (the Main Heroine/Protagonist) would have around 3-4 Routes/Love Interests: Saber, Lancer, Archer, and possibly Rider.

Father's last act
He wasn't killed instantly by Manaka, but was mortally wounded. As Saber fades away after killing his own Master in order to protect Ayaka, her father, mortally wounded and slowly dying, use this chance to seal the Holy Relic within his last daughter in order to make her the next participant in the upcoming Grail War and to keep her safe.

He and Ayaka were founded and rescued by Members of the Mage Association or the Holy Church. Though Ayaka is recovering, her father is far from being saved. In the hospital (or any place they were sent to be restored), as he slowly dies in front of the restored Ayaka, he informed her to be prepared for the upcoming Grail War, and later apologizes for not being a great father to her (as he focused more on teaching Manaka, his heir). As he believed his death is a punishment for not caring Ayaka, and tells her that it's alright for her to hate him.

Ayaka, tearfully cried out that he's wrong, she still loved him and beg him not to leave her, as he's the only family she had left now. Her father, express remorse for leaving his last daughter alone, but was able to return his love to her one last time, and reassured her that she'll be alright, as he know that Saber will come back, and he prayed that Saber will always protect her at all cost, to keep her safe throughout the end of the war. He then passed away, and seeing him die in front of her made the young Ayaka traumatized, which made her not wanting to participate in the Grail War and to see another life taken in front of her eyes (especially when she had a difficult time to sacrifice her pigeons).

The Mother of Ayaka and Manaka is a Foreigner
Possibly she's a North American or European (either a Magus or just an ordinary human who was aware of her husband's Magus life). Which probably explain why Manaka's hair color is blond, she must have inherited it from her mother, while Ayaka inherited her hair color from her father.She may have passed away long before the event of the story (possibly died a few weeks or months after giving birth to Ayaka).
  • Confirmed. It's mentioned in the prequel novels that their mother is in fact British.

The Catalyst that is sealed with Ayaka is actually the Round Table itself
Which explains why Excalibur has thirteen seals.
  • and for something epic, in the Final Battle, Ayaka would go through her Awakening, creating a large cirle beneath her that represents the Round Table, and not only it help Saber unleashing Excalibur's true power/breaking all of Excalibur's constraints, but she can summoned the Knights of the Round Table to aid her three Servants to defeat the Beast.
  • it could be like how Sunannomon in digimon preformed his last attack. The in a humanoid abomination form rushes fowerd pushing Gilgamesh and Cu away and impales Saber. Saber looks him in the eye and sayes "this end today" he raises Excailbur and swings The Ghosts of the Knights all preform a attack (probley there noble phantasms) before Excailbur swings done.
  • While the above two would be really awesome, it's doubtful. Avalon was a central part of the original Fate's design. So it would be only natural that Ayaka still has it here much like how Shirou had it inside him for the majority of Fate/stay night. That, and it's stated to be a Holy Relic, and the only thing that comes to mind would be Avalon.
    • It's probably the relic that Manaka used as well, as Ayaka is stated to have summoned Saber because of the relic inside her. So it has to be something that's connected to King Arthur closely for that to happen. The Round Table doesn't really work as it could bring about any of the 13 knights who served the former.
    • That said, there is still a chance of Avalon being changed up since Proto-Rider was changed from Theseus to Perseus. But again, doubtful. Especially given the fact that Ayaka was stabbed by Proto-Lancer just before she summoned Proto-Saber, but the moment afterwards, there's not even a wound. Granted this could attributed to the animation itself rather than story, but the fact that their's an audible stabbing sound kinda puts a dent in that.
  • Jossed. Fragments reveals that Manaka used Avalon (though unnamed unlike FSN) as her catalyst to summon Saber, so it's likely the same catalyst that allowed Ayaka to summon Saber eight years later.

The identity of the Servants of the previous Grail War (appeared/mentioned in the Prequel Light Novel)
  • Lancer: Heavily implied to be Brynhildr = Spearwoman that wears an exotic armor, carries small red bottle and her body wrapped by fire magic.
    • Confirmed
  • Caster: Either Faust or Mephistopheles = one act mentioned that Caster wears a black mantle and also a Demon look-alike.
    • Jossed, as his identity is revealed to be Paracelsus in the Second Act.
  • Archer: Possibly Oddyseus or a Pandavan hero. His archery is compared to Sir Tristan's, and his stronger shots can shave parts of mountains off.
    • Jossed. He's Arash, a hero of Iranian mythology
  • Rider: All but directly stated to be Ramesses II, as he was alive in Moses' time, had Nefertari as his wife and has a Noble Phantasm called Ramesseum Tentyris. He also tells others to call him Ozymandias, the Greek name for Ramesses II.
  • Berserker: A legendary figure that associated with the Werewolf Legend = due to having a timed transformation, that this Servant will go to its mad enhancement (howling) at the presence of the moon.
    • Jossed. He's Dr. Jekyll and Mr. Hyde
  • Assassin: Heavily implied to be the Female Prototype-version of Hassan-I Sabbah = has grey-blue skin and wear skull mask, and can transform into cat.
    • Confirmed.

Proto Saber is more cheerful and much less angsty over his reign than F/SN's Saber because he spent centuries in Avalon in between the previous Grail War in F/P's back story and F/P's current War.
According to Proto Saber's page on the Type Moon wiki, he initially, like F/SN's Saber, wanted to use the Grail to redo the selection of the king; we can only assume that, during the previous War (and quite possibly during his reign), he was much like Arturia: using a strong, stoic exterior to hide a more vulnerable, insecure person. In the end, though, Proto Saber discovered that the Holy Grail was corrupt and wouldn't give him what he wanted, so he gave up his wish; if we assume that his reign was more or less the same as Arturia's, then he must have made the deal with the world while on his deathbed, which would have been broken after he decided to stop pursuing the Grail. Which means he would have ended up in Avalon, where he would have spent 1,500 years enjoying eternal rest and beauty and getting over any and all of his personal issues before being accidentally summoned by Ayaka.
  • While that would make sense, there's hole in that logic. If his contract is the same as Artoria's, then giving up on obtaining the grail and having his wish fulfilled would erase it, removing his ability to be summoned as a Servant as he'll go towards Avalon instead of the Throne of Heroes once he disappears. This is due to the fact the King Arthur is the "Once and Future King", considered to be still alive as a person and is only resting in Avalon, waiting for the day his country needs him again.

Proto Saber has the original version of Unlimited Blade Works.
You know how the motif of a Field of Blades, despite being the symbol of Archer and Shirou, is nonetheless prominently used to represent Saber and her angst over the Battle of Camlann? This was because it was originally intended to be Saber's motif entirely, before Gilgamesh was moved out of the War's Archer slot and replaced with an Original Generation character. One of Proto Saber's Noble Phantasms could be a Reality Marble shaped like the Battle of Camlann - or even a time-travel spell to take him and his enemies to Camlann itself. Either way, if this proto-UBW retained some of the final UBW's functionality, then it could very well act as a sort of countermeasure against Bab-ilu, furthering the rivalry Proto Saber has with Proto Archer.

Schrödinger's Player Character is at play between Prototype Arthur and FSN Artoria.
This may subvert the previous WMG suggesting that Arthur does not carry any issues about how his reign ended, unlike Artoria. That is to say, both characters exist as two possibilities: if Artoria ever gets her wish of finding someone else to pull the Sword in the Stone/become King, the story is rewritten so that a male Arthur exists and come to pass. Vice-versa, if Arthur gets to achieve his wish and move on, it is Artoria who becomes King. This would at least make sense as to how/why both versions are available to be summoned in Fate/Grand Order, although this also carries some Fridge Horror implications regarding their fates (i.e. one has to be condemned for the other to get a happy ending).
  • Except that as Fragments reveals, Arthur's wish is not to have someone replace him. Rather, it's to create an eternal kingdom of peace where the people no longer have to suffer.

Ayaka and Manaka's mother has some sort of connection to Saber

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