When a show has been on the air for as long as the Pokémon anime has, it's bound to be impacted by real-life events sooner or later. Unfortunately for fans, one of the series' biggest plotlines at the time wound up being unceremoniously canceled following one of Japan's deadliest earthquakes.
The 2011 Tohoku earthquake and its resulting tsunami did massive damage to Japan, including the Fukushima nuclear reactor, which went on to become another major disaster all its own. Many anime and manga series that were ongoing at the time were impacted as a result, and the event went on to have lasting impacts on several franchises, such as Jojo's Bizarre Adventure, which worked the earthquake into its plot. Among the affected series was the Pokémon anime, at the time in its Black and White era.
For Black and White, the series had decided to try some new things. Brock was permanently removed from the show, and Ash had a completely new cast of companions for the first time. Part of that also meant retooling Team Rocket's Jessie and James, who were no longer going to be goofy harmless villains, but instead a real threat, and with the full of Giovanni and the rest of Team Rocket to boot. In fact, the series was setting up for a major confrontation between the Unova region's own Team Plasma and the infiltrating Team Rocket. The "Team Plasma vs. Team Rocket" arc was set to be the very next episodes to air when the Tohoku earthquake hit on March 11, 2011. When the air date for the next Pokémon episode came around, however, the show skipped both episodes, with the network noting that they would be aired "someday," although they never were.
Team Rocket Caused Too Much Destruction
The plot of the Team Rocket vs. Team Plasma two-parter, so far as is known, was set to involve a major clash in Castelia City, one of the region's biggest and most populated. They were fighting over an object known as Meteonite, which had appeared in several episodes leading up to the clash. The object apparently goes wild with power, threatening to destroy the city as a result. Airing the episodes depicting destruction at the time was felt to be insensitive, so they were skipped for the time being, moving on instead to what would've been episode 25. This naturally caused some major continuity errors, and eventually the show retconned the conflict out of existence. Pokémon's Team Plasma wouldn't show up again for almost 90 episodes, and their later appearance didn't acknowledge the unaired episodes at all, instead taking things in a completely different direction based on the then-released Black 2 and White 2.
The episodes for 2 of only 3 Pokémon episodes that went unaired in Japan, with the remaining episode also going unaired for earthquake-related reasons. The Pokémon Company's decision here is completely understandable, but as fans, it's hard not to wonder what might have been had Team Rocket and Team Plasma actually had the chance to face off.