The Prophet's (pbuh) Stoning of Adulterers

Question

I recently come across the 15th verse of An-Nisa stating directly the punishment for married women who have commited adultery and it seemed to contradict the instruction of the Prophet (pbuh) to stone. I understand the flogging of fornicators (2nd verse Al-Nur) because it is a direct command just like that in An-Nisa. If God gave clear orders on how to punish adulterers why would the Prophet (pbuh) come up with another totaly different punishment? Is there a verse that instructs stoning? Did the prophet stone any adulterer?

Response

The fifteenth verse of An-Nisa was a temporary measure until the actual method of dealing with adulterers was revealed by God. It is for this reason that it ends with the phrase "(until) God ordain for them some (other) way". The sixth verse of Al-Nur is the real punishment that would apply in an established Islamic state and, as you have noted, it clearly states flogging the fornicators (including adulterers) with a hundred stripes.

As for the Prophet (pbuh) punishing the adulterers by having them stoned to death, one of the opinions is that the actual punishment of adultery is just flogging and not stoning to death. The stoning in those instances was due to the fact that the accused also created mischief in the land in addition to committing adultery, and under another Quranic injunction they would be executed for that. Please do keep in mind that this is not ordinary mischief, these people were usually rapists or habitual adulterers, directly challenged the authority of God and the Prophet (pbuh) by their such actions, and were thus considered a degree higher than an ordinary person who committed this crime. The verse of Quran under which they were ordered stoning is this:

إِنَّمَا جَزَاء الَّذِينَ يُحَارِبُونَ اللّهَ وَرَسُولَهُ وَيَسْعَوْنَ فِي الأَرْضِ فَسَادًا أَن يُقَتَّلُواْ أَوْ يُصَلَّبُواْ أَوْ تُقَطَّعَ أَيْدِيهِمْ وَأَرْجُلُهُم مِّنْ خِلافٍ أَوْ يُنفَوْاْ مِنَ الأَرْضِ ذَلِكَ لَهُمْ خِزْيٌ فِي الدُّنْيَا وَلَهُمْ فِي الآخِرَةِ عَذَابٌ عَظِيمٌ

The punishment of those who wage war against God and His messenger and strive to make mischief in the land is only that they should be murdered or crucified or their hands and their feet should be cut off on opposite sides or they should be imprisoned; this shall be as a disgrace for them in this world, and in the Hereafter they shall have a grievous chastisement. (Quran 5:33)

I find myself in alignment with this view more than the conventional view for the reasons that you have mentioned in your question. Prophet Muhammad (pbuh) did not come up with a different punishment than what the Quran says, instead he applied two injunctions simultaneously as the criminals fell under both of them. It is for this reason, I believe, that he ordered them to be stoned to death, and not just flogged.