The Shredder Strikes has some more backstory, but nothing particularly surprising if you’re at all familiar with the Splinters whole deal. Maybe if you’re used to him being A Man Who Is Rat instead of a Rat Who Is Man, but they established that previously anyway.
Anyhow, after getting a dressing down from Splinter for his overconfidence in weapon choice (which mainly exists to establish that Splinter is a very, very good
Ninja), Leo storms off in a huff, where he encounters a whole bunch of Foot Ninja, who incite them to meet their boss instead of trying to kill him as usual. Leo does, at least partly because he’s mad at his Rat Dad, and he meets Shredder. Presently out of uniform since a guy made of giant knives calling himself “The Shredder” doesn’t make for a great first impression.
Shredder tells him that, yes, he fought the turtles a bunch hit that was because he didn’t know if they were on the side of good or evil and that he is mired in a centuries long struggle against the forces that think they can control the world.
He neglects to mention that he’s the bad guy, and Shredder is definitely not the “everyone is the hero of their own story” kind of villain. But he also gives Leo a cool sword as a signing bonus.
Leo and Raph come to blows when he suggests hearing this Oroku Saki joker out, after all, he told a story with no corroborating evidence that implied he was a good guy, despite all evidence to the contrary, but then they calm down and decide to get a second opinion from Splinter who reveals “Oh… Oroku Saki? Yeah, he’s the Shredder. That guy sucks. He killed I learned ninjitsu from, even though I was a normal ass rat at the time”.
Which is enough for Leo to do yet another 180, because his moral compass is pointing every which way, and it leads to a boss rush against a whole damn lot of of Foot Ninja and also Hun, before Shredder himself shows up in a flash of lightning and says “Okay, you beat up my cannon fodder, now I’m going to kill you”.
Meanwhile those Blade looking Matrix guys keep popping up being reasonably sure the Turtles aren’t as big of a problem as Shredder