Pokémon Mystery Dungeon: Beyond the Shadows

Pokémon Mystery Dungeon: Beyond the Shadows (ポケモンミステリーダンジョン：ビヨンドタイム, Pokémon Mystery Dungeon: Beyond Time?) is a fanfiction written by MalikTH. It details the adventures of John the Charmander and Rei the Shinx in the Grass Continent, with events similar to Pokémon Mystery Dungeon: Explorers of Sky.

Differences compared to Explorers of Sky
This fanfiction establishes the fact that the story takes place in a different timeline from Explorers of Sky, the game that the story is based off of, by making some details different from said game.

Chapter 1

 * Rei was established to have tried many times to join the guild before meeting John.
 * The quotes used for Diglett's sentry duty differ from the ones used in EoS.
 * Rei saved John's life before he regains consciousness by moving his tail away from the water.
 * John was shown to have a connection with the Time Gears much earlier. His pulse races at the mere mention of them, whereas in the main games, he must be physically near them.
 * The Time Gears began to get stolen by Grovyle much earlier, before the events of the fanfiction even begin.
 * Sharpedo's Bluff was revealed to be Rei's home much earlier, before he and John even join the guild. Furthermore, they stay that night at Sharpedo's Bluff before joining the guild the next day, rather than joining the guild the same day as recovering the Relic Fragment.

Chapter 2

 * It was established that only guild members can use Duskull's Bank.
 * The Ten Rules for Exploration Teams are slightly different to remove the mention of noncanon game mechanics.
 * Rei was established to have lived in mediocre, yet livable conditions before the events of the fanfiction.

Chapter 3

 * John and Rei only needed to be woken up by Loudred once, after which the two are able to wake up on time from there on.
 * John and Rei were somewhat able to recite the morning chant the first day, unlike in EoS where they weren't.
 * Team Skull's arrival occured a few weeks after John and Rei joined the guild.
 * Team Skull was established to be trouble for the whole town, and not just Rei.
 * The Dimensional Scream could be activated at random, and not just when touching related items. This was shown when John performed the Scream while Skuntank and Koffing prepared their Noxious Gas Combo™.
 * Team Skull was removed from the guild roster after Skuntank and Koffing performed their Noxious Gas Combo™.

Discontinuation
The fanfiction's production was discontinued on December 5, 2017, with the promise of a reboot, which will retcon this fanfiction from the canon.