Obi-Wan confronts Anakin Skywalker about Padme before Revenge of the Sith in the book Labyrinth of Evil. It's one of the first times he blatantly addresses their relationship and that it's against the Jedi code. Why he turns a blind eye to it later, I don't know. This helps us understand how Obi-Wan knew so easily that Anakin was the father in Revenge of the Sith once he became Darth Vader during Order 66.

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