The Pokémon series has no shortage of side games and spin-offs, such as Pokkén Tournament, which introduced the fighter Shadow Mewtwo, and consequently a discussion about whether Shadow Mewtwo is Pokémon canon. At times, it can be unclear just how canon these titles are to the mainline areas of the franchise. Although the subject has been discussed with the game's producer, the answer still isn't entirely clear when it comes to whether or not Shadow Mewtwo is canon. As of now, the character has yet to appear in any other Pokémon game.

It can at times be difficult to tell whether a game counts as strictly canon or not. For example, many fans were surprised to find that Pokémon Legends: Arceus is in the core series given how the game was presented. Other prominent spin-offs like the Pokémon Mystery Dungeon series take place in their own canon rather than the timeline of the overall franchise.