Do Not Ever Pray Over Any of Them

What is notable is that Allah orders the Prophet (peace be upon him) — forbids him — to stand in it. This closely resembles another verse, read earlier but not discussed, verse 84 of Sūrat at-Tawbah:

What happened here is that ʿAbdullāh ibn Ubayy ibn Salūl was one of the chief hypocrites, a leader among them. The cause of his hypocrisy was that he had expected to be the leader. Before the Prophet (peace be upon him) removed to Madīnah Munawwarah, he had been marked out and appointed to become the next leader. When the Prophet (peace be upon him) arrived, he lost his bid for that leadership — whence a great animosity and hatred and jealousy towards the Prophet (peace be upon him), so that he remained a difficulty to the end. He was the man who would set rumours abroad and manufacture them. His son, however, was a good believer, a pure believer; and he loved his father. And his father — such men would make trouble openly, and then afterwards perhaps do a few things to show that they were believers still. So it was hard to say, unless one wished to be very severe, that these people were to be…

So when he died — when at last he died — subḥānAllāh, his son came to the Prophet (peace be upon him): will you come and pray over him, over my father? Perhaps Allah (swt) will forgive him. And the Prophet (peace be upon him) said: yes, I shall do it. The man was the chief hypocrite, the arch-hypocrite, and the Prophet (peace be upon him) agreed to go and pray over him, to pray at his grave. As he went, ʿUmar said: O Messenger of Allah, you cannot do this. You should not pray at his grave. The Prophet (peace be upon him) said: I shall pray at his grave. And he prayed there. And then these verses were revealed. Unlike the case of the masjid, where the verses came first, here the verses came after he had prayed. And the verse, as has been said, verse 84, is: do not pray over any of them who die, ever. Never pray. Do not so much as stand at their grave.

The Prophet (peace be upon him) had already done it. Why? ʿUmar had on several occasions said things and taken decisions which Allah (swt) afterwards confirmed in the Qur'an. But in this case, because the Prophet (peace be upon him), out of his compassion and his gentleness and his love, desiring forgiveness and good for people, said: I shall pray — for that reason Allah let him pray. Allah loves him too well. He let him pray. But immediately afterwards the ruling came down that he should not pray over any of them: that they had disbelieved in Allah and His Messenger, and had died in transgression.

Returning, then, to verse 108: here Allah tells him that he may not do it. Eventually some of the Ṣaḥābah went and destroyed the building and burnt it down. And from what the geologists say, or from what has been excavated, there is nothing left — it was probably destroyed entirely. Masjid Qubāʾ still stands, but of that mosque there is no sign, and no remnant of it whatever. It was in all likelihood wholly destroyed at that time.