Board Thread:Questions and Answers/@comment-186.68.114.226-20130219164648/@comment-5075764-20130401003211

Well, this is set in the ep after "Enemy of my Enemy", where Karai apparently makes an alliance with the turtles. I'm just guessing, but maybe during that ep, the Foot learn that April is a friend of the turtles, and therefore a friend of Splinter, and Shredder has them kidnap her to lure Splinter out.