The process of the Divine presence leaving the Temple begins with a movement from the innermost room toward the outside. God's glory lifts up and departs from the cherubim standing over the Ark cover in the Holy of Holies, moving down to the threshold of that sacred space [מצודת ציון, מצודת דוד]. Regarding the timing of this event, some identify it as the exact same departure mentioned earlier in the prophet's visions [רש״י]. Alternatively, it is possible that the Divine presence had briefly returned to the cherubim and is now leaving them once again [מצודת דוד].
This movement away from the cherubim carries a profound message. It signals that the impending burning of the Temple will not be carried out through any angelic messenger, but through the direct power and supervision of God alone. By pouring out His anger on the physical building of the Temple itself, God purposefully lessens the punishment that would otherwise fall upon the people of Israel [מלבי״ם].
As the Divine glory travels outward from the Holy of Holies, much like someone preparing to leave His home, the building fills with a dense cloud. Simultaneously, the inner courtyard through which He exits becomes filled with a brilliant glow radiating from God's glory [מצודת דוד, מלבי״ם, ביאור שטיינזלץ]. While God's presence within the cloud appears as fire and light, this outward glow in the courtyard is not the primary source of illumination. Instead, it is a reflected brilliance spreading outward from the essential light still resting inside the building, just as a radiant aura always surrounds a central flame [מלבי״ם].