My theory on Ai/Sherry/Shiho's death is that at the end of the series when the real battle against the BO begins, she's going to try commiting suicide by taking a pill. She accidentally takes a pill that causes her to lose her memory, though, so Agasa and Conan decide not to tell her about her real story. She live as Ai for the rest of her life and falls in love with Mitsuhiko.