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I had just recently finished the Carnival Phantasm series and watched the last episode called "Fate/Prototype". This episode is different b/c it looks to be about a different Fate universe. If so, is this a different anime in the Fate series?

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Fate/Prototype is the original story created by Kinoko Nasu which would later after many changes be published as Fate/stay night. It can be considered as an alternate universe to the world of Fate/stay night, in a similar way to the other Fate spinoffs like Fate/Apocrypha and Fate/Extra.

Based around the Second Tokyo Holy Grail War, it is the original concept of Kinoko Nasu's for Fate/stay night. It has yet to be adapted as a full series, with only a short animated feature and production notes detailing the story.
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The original version of Fate/stay night, now called Old Fate (旧Fate, Kyū Fate?) and Fate Origin, was a novel that Nasu wrote during high school, eventually being vastly redesigned as a visual novel to suit the target audience. They were reluctant to completely abandon many of the "original charms" that were discarded, and they had wished to utilize them somehow with each passing year. Twenty years after originally being penned, they decided to make use of the release of Carnival Phantasm, discarding other proposals like Princess Arcueid VS Saber Lily or a scene from Tsukihime 2, to "just once, return to the original" for the company's belated tenth anniversary.

See the Wiki for more information.
A good article about Fate/Prototype.

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The final disc release of the Carnival Phantasm included the Fate/Prototype OVA, which is an extra (i.e. not directly related to Carnaval Phantasm) short animation that tastes/showcases off story bits and designs for the original concept of the Fate/stay night series.

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