Or at least that's what it said on the special features and some stuf I read online. They obviously present it in a way that it stands on it's own as a "reboot" at the same time, too. So I can see how people wouldn't notice. I didn't until I heard about it this week during my recent Turtles kick.
Then there's also the whole thing where they show the trophy case at the end that includes the movie versions of Shredder's helmet, the ooze canister, and that time travel lantern thing from the 3rd movie.
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