The passuk states “ובהעלות הענן מעל המשכן יסעו בני ישראל, when the cloud ascended from upon the Mishkon, Bnei Yisrael would travel.” The Seforno says the Shechinah was permanent by the Mishkon and did not leave at all until Yisrael needed to travel. This was not so by Shiloh or by the first or second Bais HaMikdosh. However by the third Bais HaMikdosh the Shechinah will be even more permanent as it states in Zechariah, “ואני אהיה לה נאום ה’ חומת אש סביב ולכבוד אהיה בתוכה, Hashem said, ‘and I will be for it a wall of fire all around, and for honor I will be inside it.’”
The following passuk states “and if the cloud did not leave, they would not travel until it departed.” This was because “ענן ה’ על המשכן יומם, Hashem’s cloud was over the Mishkon during the day.” Onkelos translates as “the cloud of the honor of Hashem was on the Mishkon during the day.” The Nesina LaGer says, Onkelos adds “the honor” of Hashem, for the honor of the Shechinah.
The passuk ends, “ואש תהיה לילה בו לעיני כל בית ישראל בכל מסעיהם.” Targum Yonasan Ben Uziel translates “and a pillar of fire would shine during the night and all of Bnei Yisrael were able to see for all their travels.” Yonasan Ben Uziel explains that the אש mentioned in this passuk is the pillar of fire. This as it states in Parshas Beshalach, “וה’ הולך לפניהם יומם בעמוד ענן לנחותם הדרך ולילה בעמוד אש להאיר להם ללכת יומם ולילה, and Hashem would lead before them during the day in a pillar of cloud to lead them on the road, and during the night in a pillar of fire to shine for them, to go during the day and during the night.” There were two pillars, the pillar of cloud and the pillar of fire.
Onkelos translates ואש תהיה לילה בו לעיני כל בית ישראל as “and an appearance of fire would be in it during the night before all of Bais Yisrael.” The Nesina LaGer says, Onkelos adds “an appearance” for the honor of the Shechinah, just as he added “honor” at the beginning of the passuk. He understands that this was not the regular pillar of fire. It is interesting to note that he translates here exactly as the passuk states in Parshas Be’halosecha about the cloud, “ומראה אש לילה and an appearance of fire during the night.”
The Midrash Tanchuma explains: In the Midbar there were six clouds; four on the sides of Yisrael plus one above and one below. A seventh cloud led the way, during the day as a cloud, and at night as fire.
The Malbim explains that there was an additional cloud above the Mishkon, not one of the seven clouds. During the day it was a cloud and at night it transformed into an appearance of fire which was inside the cloud itself. This was unlike when Yisrael went out of Mitzrayim there were two separate and independent clouds, the pillar of cloud and pillar of fire, one served during the day and the other at night. The Chizkuni also says there was a special cloud over the Mishkon which was elevated more than the other clouds. This is as the Midrash Tanchuma says the cloud of the Shechinah which was over the Mishkon would go over the camp of the Levi’im, in middle of the other camps, during the travelling. A different cloud, the עמוד הענן, was like a beam traveling before the camps to direct them where to go and when to stop.
The Seforno adds, the passuk “כי ענן ה’ על המשכן יומם ואש תהיה לילה בו” teaches that the Shechinah was permanently by the Mishkon throughout the forty years in the desert, similar to what it states by Yom Kippur “כי בענן אראה על הכפרת, since in the cloud I will be seen on the kapores.” We see that throughout the forty years in the desert the Mishkon was like the level of Yom Kippur. The Meshech Chochmah says, the Midrash brings that for this reason Aharon was able to perform the seder avodah of Yom Kippur every day in the desert!
May Hashem return the Bais HaMikdosh with the Shechinah!