“And the glory of the God of Israel went up.” In Ezekiel’s vision, God, surrounded by His glory, that is, His glorious brightness, moves to the threshold of the Temple (when the text says “the glory of God” moved, it is assumed that the reader knows the glory is surrounding God—that He is personally present in it, so that in this context, when the glory moves, God moves. See commentary on Ezek. 1:28).
The text is not specifically clear about where God had come from when He moved to the threshold of the Temple. When Ezekiel was taken in his vision to the north gate of the Temple adjacent to the altar, God was already there (Ezek. 8:3-4). Then God led Ezekiel on a tour of the Temple and the wickedness going on there (Ezek. 8:5, 7, 14, 16). It is possible that God rode on His cherubim chariot-throne while giving that tour, and that does seems to be the natural reading of the text seeing that after the tour God moves from over the cherubim to the threshold of the Temple (Ezek. 9:3; 10:3-4).
It does not seem that God moved from inside the Holy of Holies to the threshold of the Temple, although some scholars believe that when the text says God moved from the “cherub” to the threshold that He moved from the cherubim inside the Holy of Holies to the threshold. But we learn from Ezekiel 10:3 that God had parked His chariot-throne on the south side of the Temple in the courtyard, and God’s glory had filled the inner courtyard. God apparently had come into the Temple courtyard riding on His cherubim chariot-throne and would have been “above” the cherubim on his throne (cp. Ezek. 1:26). Then He got off his throne that was above the cherubim and went to the threshold of the Temple, immediately in front of the entrance to the Holy Place.
Once at the threshold of the Temple, God issues a command to destroy Jerusalem. Most scholars agree that the threshold of the Temple is the entrance to the Temple itself, which is the entrance to the Holy Place. God did not issue His command to destroy Jerusalem from His chariot-throne even though He could have; He issued His command from the Temple itself. This is significant because He had wanted to live in His Temple among His people, but their egregious sins drove Him away, and even resulted in His command to destroy Jerusalem. God understands that people sin, but when people willfully sin against Him out of a hard and rebellious heart, He withdraws from them and their sin has terrible consequences.
What Ezekiel 9:3 says is stated again in Ezekiel 10:4, Yahweh coming off His chariot-throne and going to the threshold of the Temple. However, in Ezekiel 10 the text focuses on the glory of God—the brilliant light that surrounded God and indicated His presence—and shows how it filled both the Temple court and the Temple itself. Also, Ezekiel 10 tells us more about the “man” who will bring judgment on Israel, and that he is to scatter burning coals on Jerusalem (Ezek. 10:2, 6-7).
In summary, then, when Ezekiel arrived in the Temple in his vision, God’s cherubim chariot-throne and God were already there (Ezek. 8:3-4). Then God moved to the threshold of the Temple and gave the command to destroy Jerusalem (Ezek. 9:3-7). Then He got back on His chariot-throne and moved to the east gate of the Temple (Ezek. 10:18-19). From over the east gate, He moved to over the Mount of Olives (Ezek. 11:22-23). God and His glory will not return to a Temple in Jerusalem until the Millennial Temple (Ezek. 43:1-4). So the continual sin of Judah, and their hardheartedness, drove God away. God, surrounded by His glory, left Judah and Jerusalem, which were then destroyed by the Babylonians. [For more on Ezekiel 8-11 and what happened, see commentary on Ezek. 8:4].