I guess the Shredder Wars could've worked as an ending had the show continued.
The best way that I can imagine it happening is someone stealing the time scepter and messing with time and space.
In an alternate timeline, Shredder was victorious. At least for me, I don't think it requires a whole lot of explaining.
I assume that unlike the original Teenage Mutant Ninja Turtles movie, Foot recruits have nothing to do with the street gangs. I assume that the Foot recruit members the way that they did in Karate Schooled.
"Wait, for opportunities to present themselves."
With Shredder gone, I don't think she had a any trouble just walking away.
This would seem to imply that the US government isn't corrupt as well.
But that being the case, I just assume that the US government and The Foot never had conflicting agendas until the recovery of alien technology came about.
Maybe eventually some day Shredder would've used his big utrom brain and realized (the way that April did with TCRI) that a quick little internet search for the name "Mortu" would pop up the TCRI organization leading to the same showdown that took place in Secret Origins.
Maybe they sit around hoping that some day Nickelodeon will one day wise up and give their favorite cartoon a proper DVD release?
I don't have a hard time imagining that the Foot never recovered from the events of Wedding Bells and Bytes and Turtles Forever.