Karai was only mind controlled for 2 episodes, she didn't even appear for most of Season 3. Her early appearances were in her mindless snake form, or just captured by Shredder.
It's easy to forget how little we saw of Karai in Season 3. There was the 8 Northampton episodes, then the few snake eps she had, then the other eps just either didn't feature her or focused on the intro of new mutants like Muckman, Mondo, Creep/Snakeweed, Shredder clones, etc...and she didn't appear.
During Season 4 the first episode they get back from space she's leading the Foot with Shinigami.
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