So I recently stumbled upon this website: http://www.alexanderstomb.com/ . To summarize the site for those who don't want to go stumble around there, this historian and achaeologist, Andrew Chugg, has reason to believe that historians and archaeologists have missed a few things when looking for the tomb of Alexander and that the local Alexandrian story that it is under the Mosque of Daniel in Alexandria (which can't be confirmed since they won't allow excavation under the holy site) is actually false and that it was made up after the stone sarcophagus of Alexander was moved by the British to London in 1802. His mummified remains were not in the sarcophagus, and it had been found about 5 years earlier by Napoleon empty, and appeared to have been empty for quite some time. It being Alexander the Great here, and Napoleon being who he was, I don't think he would have lied about that.
So having gone over the surviving ancient sources on Alexander's tomb, the location of his body and the history of Alexandria, Chugg has come to the conclusion that it may have become misidentified by the time Muslim forces took over Alexandria from the Christians and that they may have by that time started venerating the remains as the remains of St. Mark, the founder of Christianity in Alexandria, much as Alexander's remains had been venerated by the pagans as the founder of Alexandria itself. In the earliest records of the death of St. Mark, he was said to have been martyred and his remains burned. Later records say that a miracle occurred and that his remains were spared from the flames and protected by his Christian followers. In 828 CE, the remains officially identified (though not scientifically identified) as those of St. Mark were smuggled out of Alexandria by Venetian tradesmen when the Arabs took the city and taken to Venice where they were housed and continue to be housed in the Basilica of St. Mark (or San Marco). I shudder to think of Alexander's remains in a city so wet and prone to flooding, not that Alexandria, Egypt was much better, but supposedly they have been moved, as flooding has grown worse in recent years, to a part of the church safe from flooding.
Now, as of July 2005, the Vatican is still refusing Mr. Chugg's requests for an investigation of St. Mark's remains to determine their date of origin, cause of death, and, in fact, if they are not the remains of St. Mark, but rather the remains of Alexander the Great... At which time, I hope they are removed to a safer, drier, more stable location. One can well imagine all the reasons why the Vatican would not want that to be proven. Mr. Chugg has information on his site about how you can help his cause to get permission from the Vatican under "St. Mark Testing."