Link lives in Kokiri Forest but he doesn't have a fairy. One day Navi the fairy comes to him. Navi tells him that the Great Deku Tree has summoned him. So Link tries to go but Mido stops him. Link finds a sword and shield, goes to the Deku Tree and enters. So same as OoT, but he gets a lantern instead of the slingshot. Link goes through the dungeon, finds Queen Gohma and kills it. But here's when the story kicks in. See Link has killed Ganondorf and saved Termina so he comes back but as a spin-off this Link is a different one, The Hero of Shadows. Dark Link has sent over shadows of people and evil monsters. So once Link kills Queen Gohma and comes out of the Great Deku Tree a dark cloud forms over Kokiri Forest. Link has to save Hyrule but every time he kills a boss or mini boss a cloud consumes the place making it a twilight place. Later after Link kills a series of bosses Zelda tells him to go to the Giant Beanstalk to the sky desert and journey far and wide destroying dark clouds. Eventually Link finds a shadow of Hyrule Castle.
Fixed for grammar and spelling errors. Sounds good, and I like how you mix elements of Ocarina of Time (basic story) Twilight Princess (the twilight) and Minish Cap (Beanstalk, maybe the shadow of Hyrule Castle as in Dark Hyrule Castle). Looks like it will turn out quite well, can't wait for more updates.