How Fate/Prototype would endMisaya, Sancraid, Caster's Master, Rider, Caster, Assassin, and Berserker are killed in the war. Ayaka has three Servants: Saber, Lancer, and Archer (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. Depending on the fate of the three Servants, they either fade away after the war, returning to the Throne of Heroes (or for Saber's case, to Avalon); or under some circumstances, they were able to maintain they existence after the Grail's destruction that they all decided to stay with Ayaka.
Ayaka's Love InterestsIf 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 actHe 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 ForeignerPossibly 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 of inherited 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).
The Catalyst that is sealed with Ayaka is actually the Round Table itselfWhich explains why Excalibur has thirteen seals.
The identity of the Servants of the previous Grail War (appeared/mentioned in the Prequel Light Novel)
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.