And a double post for a thought I had:
Would it be too much to assume that Kitsune has been pulling the strings on just about
everything?
Sure, Saki is her "star puppet", but when you think about it, she probably had to manipulate dozens of other things around her in order to get her plan into motion properly. Likely right down to getting the the murder of all six members of the Hamato family - and the fued to fuel that - to the Utroms involvement in reviving both sides of that fued so it could be brought back in a time closer to what is appropriate for her goal in bringing her father back to the Physical World. Even the collapse of Utrominion - which might seem unrelated at first - by some bends of logic, plays right into her hands.
And for some of the more conflicting elements like timing Leatherhead somehow getting on Burnow before the Turtles would end up hanging out with the pirates that culminates in Leatherhead's mutation...I have this to say:
I don't think we're done with time travel. But the next round of it would be so much different because whoever gets a hold of it is going to be so much smarter than Bebop and Rocksteady. Someone who will have some idea of what they're doing and should be able to make a seamless timeloop without causing disaster like the last two did. And by someone whose goals would be fulfilled by the time travel events happening, but would also be smart enough to manipulate that time without interacting with her duplicates in the past.
Kitsune's behind everything, I tell you! I tell you all! All because she has a really, really weird issue with Daddy going away!
At the very least, if Kitsune herself is not time travelling, she at some point may still have manipulated events across time to make things happen the way she needs them to.