After his latest escapade into the unforgiving desert Wasteland, Jak finds himself in a strange new world filled with strange new creatures. In this new world of Equestria, Jak is forced to almost relive his past life before being taken to Haven City. In this world of peace, untouched by the plagues of war and greed, Jak takes it upon himself to protect this world from such horrors, or at least until he finds a way to get back home. Separated once more from his friends (he doesn't even have Daxter with him this time) Jak is forced to make new ones. With all of this talk of "harmony" and "friendship is magic," not including the Pinkie-ness that is Pinkie Pie, it's almost enough to make Jak miss the Metal Heads...
I should also mention that this story completely ignores the events that transpired in the horrible excuse of a game Jak & Daxter: The Lost Frontier. That game was horrible and I refuse to acknowledge its credibility to the Jak and Daxter series. Also, I am not using Twilicorn in this story. This isn't because I hate the idea of Twilight as an alicorn, but just because I started brainstorming for this before the Season 3 finale and don't want to have to change everything. Jak in this story will retain all of his Dark Jak and Light Jak powers (from both Jak 2 and Jak 3), including the power to turn invisible but without the aid of a random Precursor statue.