On one particular Chinese website, I found an entry where, according to an official source, Ai would be killed by gunfire from the Black Organization toward the end, and that she would give the ultimate antidote for APTX-4869 to Conan as she is dying. It also states that Dr. Agasa is actually affiliated with the Black Organization (which I'm still not sure whether or not to believe).
If you can read Chinese, please read for yourself:
http://group.mtime.com/conan/discussion/429668/