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Actually it was kinda different. If you guys recall back then, the same 2 or so seasons of several cartoons were aired weakly on FOX and whatnot, while the newer episodes with higher animation quality and new intros were aired Saturday mornings.
If I recall, 2 main examples were the Smurfs and The Chipmunks. The Smurfs had the same batch of episodes running weekly, but the ones aired on Saturday were newer episodes and newer characters (I forgot their names, there was like a little girl Smurf and a grandpa Smurf added later on, and I don't mean Papa Smurf and Smurfette). The Chipmunks had the same batch running weekly, but the Saturday morning version had a different intro and the designs were improved, making them look like they did in the Chipmunk adventure and their cameo appearance in the Cartoon All-Stars to the rescue.
The Turtles was the very rare example in which they had the first 3 seasons running weekly, with CBS running newer episodes with a new intro and a slightly different art style and in an hour long 2 episode format, with one episode being the usual Shredder stuff and the second episode mostly focusing on one Turtle and the villain being scientists and mobsters. The difference with the Turtles and all the other cartoons like Smurfs, Beetlejuice, The Chipmunks and Muppet Babies... was that occasionally there would be new episodes appearing in the weekly format, still with the classic intro.
Offhand I can remember the Rondo episode, the Howie episodes, that giant Don VS giant ape, Shredder's mom and the two Hokum Hare episodes were new episodes running in the weekly run at the same time that CBS was still airing their new episodes with the new intro and such. That's why we had two Atlantis episodes, one was weekly, the other was the CBS one. That's also why we have 2 episodes of the bad guys surviving the end of season 3's Big Blow Out, because Plan 6 from Dimension X started new eps for the weekly run while The Dimension X Story was the series premiere for the CBS eps.
It was a case of the right hand not knowing what the left hand was doing, and the reason why the episodes are so sloppily out of order on the DVDs. After season 3 and some of 4, it really wasn't a matter of seasons anymore, it was just the weekly eps and the CBS Saturday eps. When trying to make sense of what was a season 4, a season 5 and what-have-you, whenever DVD sets became a thing, well.... I don't envy the guys in charge of having to sort through that mess. It wasn't until Red Sky kept things only on CBS that there was a clear format.
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