G-d’s presence resided within the The Ark of the Covenant

The Ark was the manifestation of God's physical presence on earth (the shekhina).

the shekhina;

Translation

God's Presence, Kingdom

Description

The Shekhinah is a Talmudic concept representing God's dwelling and immanence in the created world. It was equated with the "Keneset Yisrael," the personified spirit of the People of Israel.

According to a Rabbinic tradition, the Shekhinah shares in the exiles of the Jewish people.

Therefore, the redemption of the people of Israel is inextricably linked to the remedying of an alienation within God him/herself, introducing a bold new element into traditional Jewish Messianic eschatology.

It is through the Shekhinah that humans can experience the Divine.

The passivity of the Shekhinah is often emphasized (equated with its femininity), as the recipient of forces from the higher Sefirot.

When God spoke with Moses in the Tent of Meeting in the desert, he did so from between the two Cherubs.

Bamidbar - Numbers - Chapter 7

89 When Moses would come into the Tent of Meeting to speak with Him, he would hear the voice speaking to him from the two cherubim above the covering which was over the Ark of Testimony, and He spoke to him.

Once the Ark was moved into the Holy of Holies in the Tabernacle, and later in the Temple, it was accessible only once a year, and then, only by one person. On Yom Kippur, the High Priest (Kohen Gadol) could enter the Holy of Holies to ask forgiveness for himself and for all the nation of Israel

Vayikra - Leviticus - Chapter 16

2 And the Lord said to Moses: Speak to your brother Aaron, that he should not come at all times into the Holy within the dividing curtain, in front of the cover that is upon the ark, so that he should not die, for I appear over the ark cover in a cloud.

The relationship between the Ark and the shekhina is reinforced by the recurring motif of clouds. God's presence is frequently seen in the guise of a cloud in the Bible

Shemot - Exodus - Chapter 24

16 And the glory of the Lord rested on Mount Sinai, and the cloud covered it for six days, and He called to Moses on the seventh day from within the cloud.

and the Ark is constantly accompanied by clouds: When God spoke from between the Cherubs, there was a glowing cloud visible there

Shemot - Exodus - Chapter 40

35 Moses could not enter the Tent of Meeting because the cloud rested upon it and the glory of the Lord filled the Mishkan.

When the High Priest entered presence of the Ark on Yom Kippur, he did so only under the cover of a cloud of incense, perhaps intended to mask the sight of the shekhina in all its glory.

Vayikra - Leviticus - Chapter 16

13 And he shall place the incense upon the fire, before the Lord, so that the cloud of the incense shall envelope the ark cover that is over the [tablets of] Testimony, so that he shall not die.

G-d Said unto the Prophet Nathan in

Shmuel II - II Samuel - Chapter 7

4 And it came to pass on the same night, that the word of God was to Nathan saying:

5 "Go and say to My servant, to David; so says the Lord: 'Shall you build Me a house for My dwelling

6 For I have not dwelt in a house from the day that I brought up the children of Israel out of Egypt, to this day, but have walked in a tent and in a tabernacle.

7 In all [the places] wherein I have walked with all the children of Israel, did I speak a word with any of the rulers of Israel whom I commanded to shepherd my people Israel, saying: 'Why do you not build for me a house of cedar?'

8 And now, so shall you say to My servant, to David; 'Thus says the Lord of Hosts. I took you from the sheep cote, from following the sheep, to be a leader over My people Israel.

9 And I have been with you wherever you have gone, and I have cut off all your enemies from before you, and have made for you a great name, like the name of the great ones that are in the earth.

10 And I will appoint a place for My people, for Israel, and I will plant them, and they will dwell in their own place, and be disturbed no more; and the wicked people shall not continue to afflict them as formerly.

I can go on, and have a habit of being pithy! LOL So I’ll continue to make my point. The relationship of the Shekhinah, Ark of the Covenant, and the Holy of Holies can readily be seen.

The Ark of the Covenant was lost during the destruction of the first Temple (586 BCE) and never found, although there is a lot of published articles that says that the Ark of the Covenant was hidden in a massive tunnel complex under the Temple Mount, some have claimed that it was found, and it’s location is secret.

The accession of Cyrus the Great of the Persian Empire in 559 BCE made the re-establishment of the city of Jerusalem and the rebuilding of the Temple possible.  Construction of the second Temple started 521 BCE under Darius the Great. Ezra - Chapter 5 and was completed during the sixth year of his reign (c. 516 BCE), with the temple dedication taking place the following year.

The events take place in the second half of the 5th century BCE. Listed together with the Book of Ezra as Ezra-Nehemiah, it represents the final chapter in the historical narrative of the Hebrew Bible.

The original core of the book, the first-person memoir, may have been combined with the core of the Book of Ezra around 400 BCE. Further editing probably continued into the Hellenistic era.

Since some of the original artifacts were, according to the biblical account, lost after the destruction of the First Temple, the Second Temple lacked the following holy articles:

In the Second Temple, the Kodesh Hakodashim (Holy of Holies) was separated by curtains rather than a wall as in the First Temple. Still, as in the Tabernacle, the Second Temple included:

According to the Mishnah (Middot iii. 6), the "Foundation Stone" stood where the Ark used to be, and the High Priest put his censer on it on Yom Kippur.

The Second Temple also included many of the original vessels of gold that had been taken by the Babylonians but restored by Cyrus the Great. According to the Babylonian Talmud (Yoma 22b), however, the Temple lacked the Shekinah, the dwelling or settling divine presence of God, and the Ruach HaKodesh, the Spirit of Holiness, present in the first.

I don’t believe that the Devine Presence has ever left the Temple Mount! Because it is said in

Divrei Hayamim II - II Chronicles - Chapter 7

16 And now, I have chosen and consecrated this House that My name be there forever, and My eyes and heart will be there at all times.

Rashi’s commentary

and My eyes and heart will be: Jonathan renders (I Kings 9:3): “and My presence will rest there if My will is performed there at all times.” My eyes will be there if My heart and My will are there.

17 As for you, if you walk before Me as your father David walked, and do according to all that I commanded you, and you keep My statutes and My ordinances.

18 I shall set up the throne of your kingdom as I decreed to your father David, saying: You shall never lack a man ruling in Israel.

I found another source that says that the Shekinah never left.

Permanent Reminder of God's Presence

The Sages prophesied that after the Temple's destruction, the Divine Presence will never leave the Western Wall. For this reason, the Wall will never be destroyed. The Wall is endowed with everlasting sanctity. The Talmud (Megillah 3:3) says: "And I will make your sanctuaries desolate" (Leviticus 26:31) - this means that the sanctuaries retain their sanctity even when they are desolate. (See "Mystical Secret of the Western Wall")

The Wall is therefore a symbol of the Jewish People: Just as there have been many efforts to destroy the Wall - and yet it remains eternal, so too the Jewish People have outlived its enemies and remain eternal!

In the Torah, God assures us that the Jewish People will never be destroyed. In establishing the eternal covenant, God tells Abraham: "And I will establish My covenant between Me and you and your descendants after you throughout their generations, an eternal covenant, to be your God and the God of the descendants after you" (Genesis 17:7).

As Mark Twain wrote: "Other peoples have sprung up and held their torch high for a time, but it burned out, and they sit in twilight now, or have vanished. The Jew saw them all, beat them all and is now what he always was, exhibiting no decadence, no infirmities of age, no weakening of his parts, no slowing of his energies, no dulling of his alert and aggressive mind. All things are mortal but the Jew; all other forces pass, but he remains. What is the secret of his immortality?"

Mystical Secret

of the Western Wall

During the almost 2,000 years of the Jewish exile and dispersion from Israel, many wars have been fought over Jerusalem. All told, the city has been destroyed and rebuilt no less than 9 times - with each conqueror further attempting to obscure the glorious Jewish past.

But through the centuries, one symbol has miraculously remained intact: the Western Wall. It represents the indestructibility of the Jewish People.

Song of Songs 2:8-9

The voice of my Beloved! Behold it came suddenly to redeem me, as if leaping over mountains, skipping over hills. In His swiftness to redeem me, my Beloved is like a gazelle or a young hart. I thought I would be forever alone. But behold! He stands behind our wall, observing through the windows, peering through the lattices.

Midrash Rabba, Song of Songs 2:4

"Behold - He stands behind our wall" - this refers to the Western Wall of the Temple. Why so? Because God has sworn that it will never be destroyed.

Midrash Rabba, Exodus 2:2

Rabbi Eleazer said: The Divine Presence never departed from the Temple, as it is written, 'For now I have chosen and sanctified this house so that My name shall be there forever and My eyes and My heart will be there all the days' (II Chronicles 7:16)... Even when [the Temple] is destroyed, it remains in its sanctity... Even when it is destroyed, God does not leave it.

Rebbe Acha said: The Shechina (Divine Presence) will never depart from the Western Wall, as it is written, "Behold - He stands behind our wall" (Song of Songs 2:9).

Midrash Rabba, Lamentations 1:31

When Vespasian had subdued the city, he assigned the destruction of the four ramparts to the four generals. The Western Wall was allotted to Pangar. Now it had been decreed by Heaven that this should never be destroyed because the Shechinah dwells in the west. The others demolished their sections but Pangar did not demolish his.

Vespasian sent for him and asked, "Why did you not destroy your section?" He replied, "By your life, I acted so for the honor of your empire; for if I had demolished it, nobody would know (in the time to come) what it was you destroyed; but when people look at the Western Wall, they will exclaim, 'Behold the might of Vespasian from what he didn't destroy!'" From the Discovery Seminar Sourcebook