Fate/Prototype is a digest version of Kinoko Nasu's original version of Fate/stay night that he developed as a novel in high school before completely redesigning it as a visual novel. It is a twelve minute anime segment released with Carnival Phantasm Season 3, and included the Prototype Material databook. There are no current plans to develop any more pieces of media based on the concept.
It will follow the original main characters, Ayaka Sajyou and Saber, before they were changed to Shirou Emiya and Saber. Unlike from Fate/stay-night, the Prototype version had master that possessed their "Master Degree", which are named following the angelic hierarchy starting from the 7th Order and up (so Princes, Powers, Virtues, Dominions, Thrones, Cherubim, Seraphim)
Master (with Master Degrees and Servant)
Ayaka Sajyou (沙条綾香, Sajyou Ayaka) is the Master of Saber in Fate/Prototype. She is the archetype version of Shirou Emiya who was to be the protagonist of the original Fate/stay night novel that was never finished. She was originally detailed in Character Material, and she has been given an expanded role in Prototype. She is one of the Seven Masters in the Holy Grail War.
Misaya Reiroukan (玲瓏館美沙夜, Reiroukan Misaya) is the Master of Lancer in Fate/Prototype. She is the archetype version of Tohsaka Rin. She is the Second Master of the Holy Grail War.
Misaya is the version of Rin Tohsaka that was to be used in the original Fate/stay night novel that had been penned but was left uncompleted. In Prototype, information on her has been expanded to show she has savage black dogs as her familiars along with her summoned Servant, Lancer. They worked together in tandem in order hunt down another potential Master, Ayaka Sajyou and kill her.
Saber's identity is that of King Arthur Pendragon of legend. When the time came to redesign the characters on Takeuchi Takashi's suggestion Kinoko Nasu switched Arthur's gender who would then become the Saber seen in Fate/stay night.
From the small amount of screentime given, Arthur seems to have none or nowhere near most of the issues that plague his counterpart, Arturia. He is seen as playful as he teases Ayaka by removing her glasses and smiling at her. Despite this, upon revelation of the Grail System and its function, he killed his previous master and threw her into the Grail, showing a level of anger and retribution only Arturia's Saber Alter form possessed as even when faced with Emiya Kiritsugu's malicious tactics she did not raise her blade against him.
NOBLE PHANTASM
Saber has Excalibur and Invisible Air much like his counterpart. His version of Excalibur is bound by thirteen constraints placed upon it by the Knights of the Round Table, and the conditions must be met in order for the constraints to be released. Against Archer's EX Ranked Noble Phantasm, Enki, its full power was released, allowing it to evaporate the water and bisect the "Star of Destruction."
The art for Excalibur was designed by RAITA, and it is also far more ornate
Saber's ExcaliburAdded by Zahadrin and broader in its details than the Arturia's version. There is a haloed cross above the hilt with a blue and gold frame along with a line of 9 receding golden diamonds that run the length of the blade before ending near the point. In the Fate/Prototype material, there is another design that looks closer to Arturia's version.
It is unknown if Avalon exists in Prototype, but it is said that Ayaka was able to summon him due to having a holy relic buried within her to act as a catalyst much like Shirou.
Lancer seems to fill much the same role as he did before, tracking down the main character in order to eliminate them. While for his counterpart this seemed to be motivated by Shirou witnessing his battle with Archer, in Fate/Prototype Ayaka Sajyou appears to be a predestined Master for the war, leading Lancer to hunt her down. Lancer pierces Ayaka, however unlike her counterpart Ayaka summons her Servant in this instant, leading to Saber's summoning that seemingly negates any harm from his attack.
Sometime later on during the Grail War, Misaya would die due to a curse that had been inflicted upon her. Masterless, he forms a contract with Ayaka, who had lost Saber to Berseker's Master, Sancraid Phahn. It would be here that he would fight off both Berserker and Saber, corrupted and presumably the original version of Saber Alter, while Ayaka takes on the twisted priest who stole her Command Seals to reclaim Saber.
-SOURCE TYPEMOON WIKI-