I just thought of something. We could always have a fic where in GGGoH, it was green kryptonite, but when Luthor gets Kryptonite, it is for some reason red. So he makes the Superman cage from Red Kryptonite. It does not capture Superman, but it alters him in some way.
Most likely he goes and tells Lois the full truth. Personally I really don't get why Clark did not tell Lois "I'm Superman" in "Individual Responsibility".
