I present my master work: the Legends Canon trilogy! All occur in the Pokemon Special universe, and probably aren't the sort of stories that you know.
Part I: Legends of Arceus. A far-past prequel for the series, written in the style of a high-fantasy epic adventure novel. Very lore centric. A heavy read. Link: https://www.fanfiction.net/s/14099022/1/Pokemon-Adventures-Legends-of-Arceus
Part II: Brick Bronze. Taking place one year after the events of Sun and Moon, Brick Bronze follows the second rise of the Dark Lord and the War against the Eclipse Alliance by the Pokedex Holders and the Association. In the middle of a writing remake, the ending is somewhat unsatisfactory. Link: https://www.fanfiction.net/s/14091310/1/Pokemon-Adventures-Brick-Bronze
Part III: Sword and Shield. Occuring fifty-two years after the events of Brick Bronze, it is based on the comics. WIP. https://www.fanfiction.net/story/story_edit_property.php?storyid=14154917
Enjoy! Legends of Arceus is, in the writers opinion, (me) the best story.