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1Sa 5:1 Now the Philistines had taken the ark of God, and they brought it from Ebenezer to Ashdod-
This continues the theme developed in 1 Sam. 4 of how having the ark as mere religious symbolism was not the same as having relationship with God. It was taken away from Ebenezer, the rock of help, for God was no longer their rock; see on 1 Sam. 6:15; 7:12. And yet misusing it was going to bring judgment. This was relevant encouragement to the exiles as they mourned how the temple vessels had been taken to Babylon and were being misused, as in the drinking feast of Dan. 5. "Ashdod" is a form of the word translated "spoiler" or "robber" frequently used of Babylon (Is. 33:1; Jer. 4:13,20; 6:26; 9:19 and often). These historical records were intended to be discerned by the exiles as speaking to them. 

This journey of 60 km. was surely done without the ark being carried by Levites. Uzzah was later slain for just steadying the ark; whereas Samuel appears to have slept next to it, and here the Philistines manhandle it on a long journey. Uzzah was slain but they weren't. Again we see how boundaries of holiness are relative, and God looks at the heart; something clearly was very wrong in Uzzah's heart, in a way it was not wrong in the hearts of the child Samuel or these Philistines. Attitude and heart are paramount in God's judgment of men.  

1Sa 5:2 They took the ark of God into the house of Dagon and set it beside Dagon-
This connects with how the Babylonians took the temple vessels into the houses of their gods in Babylon. 

1Sa 5:3 When the people of Ashdod arose early the next day, Dagon had fallen on his face to the ground before the ark of Yahweh-
The phrase 'fell on his face to the ground before' is usually used of worship. Although the ark was indeed just a wooden box, God would not be mocked, and expressed His wish that the Philistines would quit their fish god Dagon and worship Him. See on :12. But laying flat on his face before the ark could suggest Dagon has been slain by Yahweh. There are virtually no undamaged statues of gods or idols discovered by archaeologists- because it was normal for the victors to damage or mutilate the idols of their enemies. This is what Yahweh is doing here to Dagon, as if He has won and is now mutilating the opposing god. And yet Yahweh's people had been slain before the Philistines and Dagon their god. We see here the paradox- it was a "magnificent defeat" just as was the cross. Apparent defeat is actually Yahweh's longer term victory. His people may be defeated on earth, but He wins in Heaven; and that is a theme of the book of Revelation.

In the context of the exiles, the gods of Babylon were likewise judged- "Bel bows down, Nebo stoops" (Is. 46:1). Again we see how the ark narrative in 1 Sam. 4-6 was probably rewritten for encouragement to the exiles. And to teach them that the ark's presence amongst them was not of essential importance. Rather were they to see God's personal presence in their heart, according to the promises of the new covenant they were offered.

They took Dagon and set him back in his place-
This need to "set him back in his place" connects with the mockery of idol worship found in the restoration prophets. The same phrase is used in :11. The worshippers of Dagon had to return their god to his place by themselves; but the ark was returned to its place by God working through the oxen and cart, which represented the cherubim. 

1Sa 5:4 When they arose early the next morning, Dagon had fallen on his face to the ground before the ark of Yahweh and the head of Dagon and both the palms of his hands were broken off, lying on the threshold. Only Dagon’s torso was intact-
A fish has no head, palms nor hands. The idol image was reduced to all it was- a mere fish. We saw on :3 that the phrase 'fell on his face to the ground before' is usually used of worship. It was God's intention that the Philistines come to acknowledge His supremacy, and perceive their idols for what they were, stripped of all they had added to them. "Torso" is not in the original; literally, "only Dagon was left to him".

1Sa 5:5 Therefore neither the priests of Dagon nor anyone who comes into Dagon’s house will tread on the threshold of Dagon in Ashdod, to this day-
The Philistines are therefore those who jump over the threshold, but that term is used to describe the priests of Yahweh's temple who were no better (Zeph. 1:9 "In that day, I will punish all those who leap over the threshold, who fill their master’s house with violence and deceit"). The priests may particularly be in view, whose master was Yahweh and whose house, the temple, they had defiled by their idolatry. The idea is that the temple of Yahweh had been effectively turned into that of pagan gods- despite Josiah's apparent reforms. This whole message is a stern warning against mere tokenism in repentance and reform, and challenges to the core all our self-examination and the results thereof. These priests were filling Yahweh's house with the rewards of their violence and deceit. Typical of the prophets, Zephaniah focuses upon the apparently negligible (the personal gains arising from deceit) rather than what we might consider the more obvious issues of offering children to Moloch.

1Sa 5:6 But the hand of Yahweh was heavy on the people of Ashdod and those nearby, and He destroyed them, afflicting them with tumours-
This is the reference of Ps. 78:66, which refers to how the ark was taken from Shiloh in Ephraim into the land of the Philistines, who were smitten in their private parts with tumours; but then the ark was returned, not to Shiloh in Ephraim, but to Kirjath Jearim in Judah, and thence to Jerusalem in Judah. But the question for us is the degree to which God ordered this transfer of the ark from Shiloh to Jerusalem (as the pro-Davidic author of Ps. 78 claims); or whether David manipulated it that way, and God went along with it.

1Sa 5:7 When the men of Ashdod saw what was happening they said, The ark of the God of Israel must not stay with us, for His hand is severe on us and on Dagon our god-
This was a tacit recognition that the God of Israel was real, and was greater than their god Dagon. Yet like many, they preferred to trundle along undisturbed in their religious ways, even when they had been demonstrated as false and the true way offered to them. They didn't want His abiding presence to continue with them; for "stay" is the usual word used for God's dwelling or abiding amongst His people.

1Sa 5:8 They sent therefore and gathered all the lords of the Philistines together and said, What shall we do with the ark of the God of Israel? They answered, Let the ark of the God of Israel be carried over to Gath. They carried the ark of the God of Israel there-
As noted on :7, they could have had the presence of Israel's God amongst them, but they chose not to. The language recalls how the Gentile inhabitants of the land asked the Lord Jesus, the true ark, to leave them- even when He had done great miracles amongst them (Mt. 8:34).   

1Sa 5:9 But after they had carried it there, the hand of Yahweh was against the city, causing panic, and He struck the men of the city, small and great, and tumours broke out upon them-
I suggest that this was not because God didn't want the ark nor His presence to be amongst them. He did. The punishment was because they were misusing the ark. "Tumours" were the punishment for  disobedience to the covenant (Dt. 28:27). The Philistines were being punished in this way because they had been called to accept Yahweh's covenant but had refused, as noted several times throughout this chapter.

1Sa 5:10 So they sent the ark of God to Ekron. As the ark of God came to Ekron, the Ekronites cried out, They have brought the ark of the God of Israel to us, to kill us and our people!-
Perhaps the thought was that Ekron worshipped Baal Zebub and not Dagon, and therefore the ark of Israel's God would be vanquished by that god (2 Kings 1:2). But the entire Philistine confederacy knew that they were spiritually beaten before Yahweh. Literally, as in :11, “to me, to slay me and my people” (as AVmg.). The implication is that this was a message from the god of Ekron, tacitly recognizing that he was no match for Yahweh. See on 1 Sam. 6:9.

1Sa 5:11 They sent therefore and gathered together all the lords of the Philistines, and they said, Send away the ark of the God of Israel, and let it go back to its own place so that it does not kill us and our people. For there was a deadly panic throughout all the city; the hand of God was very heavy there-
The Philistines knew the story of the Exodus (1 Sam. 4), and now they perceive that the ark represents Israel; they reason that they should let it go, and give it gold and silver, lest they suffer worse plagues and the fate of the Egyptians who refused to let Israel go. The story of the ark's journey into exile from Shiloh and return to Jerusalem therefore speaks of Judah's exile and return; see on 1 Sam. 4:22. The ark narrative material in 1 Sam. 4-6 is clearly a literary unit, perhaps edited under inspiration in the exile. The exile and return of the ark becomes the exile and return of God's people, although they returned without an ark and without the visible shekinah glory. That physical religious symbolism was replaced by them, people, the people of God, with His presence in their hearts.

See on :10; 1 Sam. 6:20. The same phrase for "go back to its own place" is used in :3, where the worshippers of Dagon had to return their god to his place by themselves; but the ark was returned to its place by God working through the oxen and cart, which represented the cherubim. 

God's experience with Israel led to His humiliation before the nations. Seeing the ark represented the very presence of God, the capture of the ark was in a sense the capture of God (1 Sam. 5:7,11 cp. 4:7). Ps. 78:61 comments: "He delivered his power to captivity, his glory to the hand of the foe". And likewise at the cross, crucifixion meant humiliation in some sense. But the point for the exiles to understand from this record was that even in captivity, Yahweh was still alive and active, and would not be mocked. We too are to personalize the history of Israel and see it speaking to our situations.

1Sa 5:12 The men who didn’t die were struck with the tumours, and the cry of the city went up to Heaven
A cry going up to heaven is the language of God's sensitivity to situations upon earth. The subtext is clearly that God was sensitive even to the sufferings of His Gentile enemies. And as noted on :3, it was God's desire that the Philistines repented. He was not at all heartless towards them.