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According to one opinion the Ark was taken to Babylonia at the time Nebuchadnezzar conquered Jerusalem and exiled King Jeconiah and the upper classes. (He then placed Jeconiah’s uncle Zedekiah on the throne for another eleven years, until the final invasion and the Temple’s destruction.) This is implied by II Chronicles 36:10 which states that King Nebuchadnezzar exiled Jeconiah to Babylonia “with the precious utensils of House of God.” (See also Isaiah 39:6.)
According to a second opinion, the righteous King Josiah, knowing that the Temple would shortly be destroyed, had the Ark hidden away. (Some of the other special items which had been kept with the Ark were also hidden – such as the jar of Manna (Exodus 16:32-34), the anointing oil (Exodus 30:22-33), and Aaron’s staff which had blossomed (Numbers 17:25).)
Where was the Ark hidden? We have no tradition that it ended up in Ethiopia (as is claimed by the Ethiopian Orthodox Tewahedo Church), and it certainly wasn’t placed in a warehouse in Washington D.C. Rather,our daf records the following incident:
A Priest was once in one of the side chambers of the Temple, designated for the storage of wood. He noticed a stone which had clearly been tampered with (and wasn’t aligned with the others). He suspected that the Ark had been hidden there. He ran over to tell his fellow but died suddenly before he could complete his account. (Thus, it became known roughly where the Ark was hidden but not precisely, and the people understood that its whereabouts was intended to remain secret.)
Another opinion in the Talmud states that the Ark was hidden in its place in the Holy of Holies, in the ground underneath it.