I agree this development was very rushed, and there should have been a scene showing how this happened, especially since Karai was losing her mind. The next thing you know she's not only completely normal in appearance (which she hadn't been even in her "human" form since her mutation), but fully in control of herself. I guess the people in charge wanted to give a sense of hope that deep down inside, Karai can still be salvaged, whereas if they started her in her serpent form, it might give the impression that Karai was lost for good. (Plus kids would think "human Karai" is good while "snake Karai" is evil.) It also "solves" the problem of how she would be strapped down to that table is she wasn't cured, but this "solution" raises more problems than it causes.
I think it would have made more sense if it had been shown that Karai was starting to get her shapeshifting power back due to a delayed reaction from the retromutagen and Stockman's ineffective tinkering (from trying to cure his own mutation), then Shredder had used the mind control worm on her in mutant form to force her to assume humanoid form but not able to get there completele. That way there would be a little ambiguity as to how much he really did want his "daughter" back (but because he's evil he still uses force and trickery). Now, they're just turning him down the old-school cartoon villain path.
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