From Bulbapedia, the community-driven Pokémon encyclopedia.
Filler episodes are used by anime and other TV shows to extend the time between the individual plot points of the major story arcs, or between the end of one major story arc and the beginning of another. A filler episode is one in which nothing happens to affect the progress of the long-term story arcs or to develop the main characters, and no returning side characters, or other significant persons (other than the main characters), appear.
Any episode during a filler arc may also sometimes be described as a filler episode. A filler arc is a storyline (often, though not always, shorter than the regular arcs) in which, over a number of episodes, an adventure is detailed that is unrelated, or tangential, to the main story arc(s); often, the filler arc adventure does not derive from the original source material. Episodes in which permanent changes or character development occur can happen during a filler arc.
In manga-based anime, fillers have been used to put distance between the anime and its source material, preventing an overlap which would cause trouble for both forms of the series. Filler episodes may follow a formulaic (and often predictable) plot, loosely based on a main episode, which will either enter the backstory of a certain aspect of a show or tell a completely new tale involving the main or supporting and even one-shot characters from previous episodes. Fillers also may introduce aspects that may complement or contradict the canon of the original source. It is not uncommon for filler story arcs to be used within a series in order to fill an episode count and subsequently build up to a main story arc.
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The Path to the Pokémon League is the first episode considered a "filler" episode in the Pokémon anime. The 36-episode Orange League arc, which accounted for the delayed release of Pokémon Gold and Silver, can be considered a filler arc. Despite this, Ash and Misty both obtain Pokémon they continue to use, though Ash's team is back to what it was at the end of Kanto when he travels to Johto. Many other important events also occur during this saga, for example Charizard beginning to obey Ash.
Infamously, the third, fourth, and fifth seasons, set in the Johto region, contain the most filler episodes of any saga. These episodes, including the 13-episode arc in the Whirl Islands, served as a way to buy time for the releases of Pokémon Ruby and Sapphire. The large number of one-off filler episodes is likely due to the cancellation of the GS Ball as a major plot device, which would have debuted Celebi and consumed a large portion of the time spent in Johto, in favor of featuring Celebi in the fourth movie instead.
When the Advanced Generation series started, filler episodes were reduced due to the introduction of Pokémon Contests. As with the Kanto saga, however, Hoenn was followed by what some consider a "filler arc", Pokémon: Battle Frontier, which built up for the arc corresponding to Pokémon Diamond and Pearl. Despite some considering Pokémon: Battle Frontier a "filler arc", many important events took place within the season, similarly to Pokémon: Adventures in the Orange Islands.
The Diamond & Pearl series had fewer filler episodes than the previous two sagas, Johto League and Advanced Generation, but is occasionally criticized for the year long gap between Ash's seventh and eighth Gym battles. It is often alternatively seen that due to the vast supporting cast featured in Sinnoh, and the focus on character development in humans and Pokémon, the episodes which are deemed "filler" are not exactly so. For example, the conclusion of the Team Galactic arc, Dawn's last Contests, and the Sinnoh Grand Festival were all aired during this gap.
The Best Wishes series also had fewer filler episodes than previous sagas, mainly due to the speed of the series and the focus on character development, similar to the Diamond & Pearl series. Another "filler saga", the journey through the Decolore Islands in Pokémon BW: Adventures in Unova and Beyond, was released towards the end of the Best Wishes series. However, unlike previous "filler seasons", this arc had fewer major events due to the absence of any kind of League. The only important events that happened during this arc were Professor Oak catching a Rotom, and Alexa joining Ash and company. Similarly to the Pokémon: Adventures in the Orange Islands, this arc was likely made to buy time for the release of the next games, in this case, Pokémon X and Y.