This may be a silly question. After the temple was rebuilt, what did the Israelites use for the missing ark of the covenant in the Holy of Holies? Or was the Holy of Holies an empty room after that?
This is an interesting question. There are many traditions and stories about the ark of the covenant; many of which are fanciful. Some claim it exists in Ethiopia inside of a church. Others claim that it resides in the Vatican in Rome (due to the clue that was left on the Arch of Titus in Rome, depicting the vanquishing of Jerusalem and the carrying away of the sacred articles of the temple—although no ark is depicted).
The last mention of the ark of the covenant chronologically is in 2 Chronicles 35, during the reign of Josiah (about 30 years before the destruction of the first temple [Solomon's]). The conventional thinking is that the Levites carried it out of Jerusalem before the Babylonian invasion and captivity to a secret place where they maintained vigil over it (sort of like the legends of the Holy Grail).
At any rate, it is thought that the Holy of Holies of the second temple (this designation refers sometimes to the rebuilt city and temple under Zerubbabel, as well as the later reconstructed and enlarged temple of Herod) was empty (containing no ark). It contained only a slab of stone upon which the ark would have sat, and that's the slab of stone that the priest would come in and sprinkle on the Day of Atonement. There are several reasons for this, including the fact that Herod was the one who rebuilt the temple to appease the Jews and magnify himself, so it was, in one sense, a defiled place. But when Rome conquered Judea in 63 B.C. as part of the Roman Empire, Pompey was surprised to find the Holy of Holies—in Zerubbabel's temple—empty!
There may be another clue to this, however. According to the Temple Institute in Jerusalem, presently, the ark of the covenant is still where it always was—underneath the stone pavement of the temple mount. According to tradition, Solomon foresaw the invasion of Jerusalem and the destruction of his temple (which is true and evidenced by his prayer upon the dedication of the temple). This tradition also mentions the building of an elaborate maze of underground tunnels deep inside the temple mount. He built these so the sacred vessels could be kept when the invasion took place. According to the Jewish Mishnah, during the reign of King Josiah (as I mentioned above, about 30 years before the destruction of the first temple), the Levites were commanded to hide the ark of the covenant in the place Solomon had prepared, since the king could see his nation weakening and the Babylonians showing interest in worldwide domination. According to the Temple Institute, they claim to know exactly where that chamber is, and that the ark is there today, waiting to be revealed again at some later point. This could be one of the reasons the Holy of Holies was indeed empty during the time of the second temple and just a slab was there. In effect, it was there, in the Holy of Holies, but it was below the elevation (essentially a couple of stories down—in the basement). It was kept there because of the uncertainty of Roman occupation.
A few years ago, a team of researchers and archaeologists attempted to be granted permission and gain access to dig under the temple mount but was met by rioting masses on the temple mount by Muslims (many of whom deny the existence of the temple). So, in effect, God could be using the Muslims to preserve it in the same spot Solomon had Josiah place it so many years ago. Interesting thoughts.
Skip Heitzig is the founder and senior pastor at Calvary Albuquerque. His teachings are heard across the country and around the world on The Connection. Skip and his wife, Lenya, and son and daughter-in-law, Nathan and Janaé, live in Albuquerque, New Mexico. Skip and Lenya are the proud grandparents of Seth Nathaniel and Kaydence Joy.