With the third anniversary of the Tohoku earthquake and Fukushima nuclear disaster coming up in under a week, and thus the cancelled airings of the Team Rocket VS. Team Plasma! (Part 1) and (Part 2) episodes, I've been thinking about the subject a lot lately.
A common sight to this day is the claim that when the earthquake and nuclear disaster happened, those two episodes getting banned as a result led to a situation where the writers' plans for Best Wishes were irreparably broken. This idea would suggest that multiple upcoming appearances of Team Plasma were abruptly cancelled, leaving Best Wishes with no ongoing story except for Team Rocket being shoehorned in where Team Plasma was.
I want to lay out why that's impossible, and propose an alternate explanation that would initially seem unlikely for why those episodes and the original form of Team Plasma never came to be.
First, the notion that content of episodes can simply be cancelled, removed and replaced on short, abrupt notice is simply not feasible. A primary example of why is this link. This link lays out concept art from BW020, which was obtained five months before the episode even aired. To get right to the point without getting bogged down in details, the episodes have to be in some stage of production, whether it be animation, scripting or recording, far in advance of the episode's airdate. To remove large amounts of content - such as hypothetical Team Plasma appearances - would cause long delays before the episode would once again be ready to air. Only one episode, the Fishing Tournament episode, was delayed then aired after the earthquake - and it was delayed for 11 weeks, from BW026 to BW037, just to make minor edits to better fit Bianca in the episode's new placement. If minor edits such as those take so long to do, large edits such as removing and replacing Team Plasma would cause much longer delays.
There are other factors involved in how long the gap between conception of an episode and airing it are, but I don't want to mistakenly talk about things I'm not familiar with enough. The long and short of it is that in March of 2011, episodes were either complete or nearly complete up to the Battle Subway two-parter, with episodes up to roughly Twist Mountain in some form of production. That would mean that Team Plasma could not have appeared until after then, which would be in the high BW070s. Everything to that point, the Don George tournaments, Team Rocket being the main villains, everything - none of it was actually affected by the earthquake. Had March 17 and March 24 gone off without problems, everything after that would have been exactly the same. Team Plasma were never going to appear in the episodes after that.
So what got those episodes and original Team Plasma banned, if not the earthquake? I'd suggest, of all things, Pokemon Black 2 and White 2 being created.
Look at where the episodes that were in development in March 2011 seem to have left off: roughly at Twist Mountain, right after which was the Brycen Gym battle. It was directly after that point that the content of the anime took a hard left turn into promoting those games, beginning with Pokestar Studios and the bizarrely shoehorned Roxie two-parter despite Drayden being teased in the Brycen episode. And right after that, of course, was Best Wishes Season 2, culminating in a Team Rocket plot centered on three new Formes introduced in the new games.
I would suggest this, based on pure speculation: had B2W2 not existed, had it been simply "Gray" like most speculated, the skipped Team Rocket VS. Team Plasma episodes would have aired sometime shortly after Brycen's Gym. After that, once the episodes reached the numbers that ended up falling into Season 2, Team Plasma would have appeared as normal - the likely intention having been to wait to this point for them all along - and a longer arc would have played out, likely ending in a Team Rocket VS. Team Plasma rematch. The League probably would have happened much later because of the nonexistence of Episode N, meaning Da! may not have existed either.
In other words, it was not the earthquake and nuclear disaster that wrecked Best Wishes's pacing and plot. It was the sudden, unexpected creation of sequel games instead of a traditional "director's cut" game, games that so drastically changed the narrative the anime had to promote that it only could toss out everything it had possibly intended to do in its second half in order to keep up with promoting said games.
