While his brothers dismissed canon!Mikey when he tries telling him about the Kraang being aliens instead of just Men in Black, chocking it up to Mikey being Mikey, here April was also there when it happens. Since April vouches for him with a piece of the Kraang's human face as evidence, they believe them much sooner.
While the canon!turtle's attempts at preventing April's kidnapping fail, having to break her out at a Kraang facility, here they manage to save her.
Kirby is still kidnapped despite the Hamatos saving April.
Paper-Thin Disguise: While it takes her a minute, it doesn't take long for April to recognize Donatello beneath his mask, easily figuring out the rest of them from there.
