Christian missionaries and other anti-Islamic polemics try to question the authority of the Quran by misinterpreting the following Hadith about the punishment of stoning.
----------------"In the meantime, 'Umar sat on the pulpit and when the call makers for the prayer had finished their call, 'Umar stood up, and having glorified and praised Allah as He deserved, he said, "Now then, I am going to tell you something which (Allah) has written for me to say. I do not know; perhaps it portends my death, so whoever understands and remembers it, must narrate it to the others wherever his mount takes him, but if somebody is afraid that he does not understand it, then it is unlawful for him to tell lies about me. Allah sent Muhammad with the Truth and revealed the Holy Book to him, and among what Allah revealed, was the Verse of the Rajam (the stoning of married person (male & female) who commits illegal sexual intercourse, and we did recite this Verse and understood and memorized it.
Allah's Apostle did carry out the punishment of stoning and so did we after him. I am afraid that after a long time has passed, somebody will say, 'By Allah, we do not find the Verse of the Rajam in Allah's Book,' and thus they will go astray by leaving an obligation which Allah has revealed. And the punishment of the Rajam is to be inflicted to any married person (male & female), who commits illegal sexual intercourse, if the required evidence is available or there is conception or confession." (Bukhari, Hadith 6328) ------------------

The problem with all these anti-Islamic polemics is that they only pick up a tradition or two and base all their arguments on their own explanations not understanding that Islamic treasury of traditions is quite rich and well able to expose any self styled hallow research scholar. Let's make a detailed study of the issue at hand.

Truth about the origin of the alleged verse:

Some traditions suggest that the wording of that verse is 'When a married man or woman commit adultery stone them (to death)'. But the fact, which becomes evident looking at all the various traditions, is that this was never meant to be part of the Quran. The word 'revealed' is used about this only in a metaphorical sense. This was perhaps a verse from one of the Books of the Jews and it was not revealed as a part of the Quran but its order was upheld through revelation so it remains in place.

The following tradition recorded by Tabari in his Tafsir points to the fact that it was a part of earlier revelations.

Ibn Jarir Tabari relates in his commentary of Surah Maida in connection to the incident of stoning of Jews."
The Holy Prophet (pbuh) said to them: 'Who is the most learned of the Law among you?'. They replied, 'so and so Al-A'war (i.e. Abdullah bin Souriya)'. He was called upon and he came. So the Prophet (pbuh) said: 'Are you the most learned of the Law among them?' He said, 'Jews think so.' So the Prophet (pbuh) said to him; 'By Allah and by the Law that He gave Moses on the day at Sinai, (tell me) what you find in the Law regarding adulterers?' He said: 'O Abul Qasim (i.e. Prophet), they stone the despicable (adulterer), and make the rich (if he does it) sit on the camel, blacken his face and make him face camel's back and stone the despicable if he commits adultery with a rich woman and they do the same to her.' So (again) the Prophet (pbuh) said to him: 'By Allah and by the Law that He gave Moses on the day at Sinai, (tell me) what you find in the Law?' He started to beat around the bush and the Prophet (pbuh) urged him by Allah and by the Law that He gave Moses on the day at Sinai till he said: 'O Abul Qasim, 'When a married man or woman commit adultery stone them.' So the Prophet (pbuh) said: 'It is like that, take them (the Jews who committed adultery) and stone them.' (Tafsir Ibn Jarir Al-Tabari 10/328 Narration 11976)

Now it's clear this verse as Abdullah bin Souriya spoke is similar to a verse in the Law (i.e. Torah). Even today we can find similar injunctions in the Bible i.e. Deuteronomy 22.

Meanings of the Hadith in question:

Let it be known that in Islam revelation is not only what constitutes the Holy Quran, infact there were other revelations as well as Holy Prophet (pbuh) did not speak on his own. (Quran 53:3)

Having said this, now lets analyze the wording of the Hadith in question.

Firstly it says, 'Allah sent Muhammad with the Truth', here 'Truth' refers to all forms of revelation i.e. both Quran and Prophet's sayings. Next we read, 'and revealed the Holy Book to him', here the first word is 'and' which is used as i.e. in conjunctive sense (separating the two phrases) and it continues 'revealed the Holy Book to him' i.e. the Quran. Then it reads, 'and among what Allah revealed, was the Verse of the Rajm (stoning)', here 'what Allah revealed' includes both types of revelation and not only the Book as we again have the conjunction 'and' separating the two phrases. And we do find the 'verse' about stoning in a saying of the Holy Prophet (pbuh):
Narrated by 'Ajma, she said: I heard that Messenger of Allah say; 'When a married man or woman commit adultery stone them both to death.' (Tabarani Kabeer, Hadith 20321. Ibn Hajr graded it as Hasan in his work Muwafaqatul Khubr al-Khabr 2/304. Same is found in al-Mustadrak, 8070. Hakim classified it as Sahih. al-Dhahbi agreed with him)

It was never meant to be a part of the Quranic text:
There are more proofs that it was not at all meant to be the part of the Quranic script.

1-It is reported in a narration from Kathir bin Salt that: Zaid (b. Thabit) said: 'I heard the Messenger of Allah say, 'When a married man or woman commit adultery stone them both (to death)', (hearing this) Amr said,
'When this was revealed I came to Prophet and asked if I could write it, he (the Prophet) disliked it.' (Mustadrik Al-Hakim, Hadith 8184. Hakim called it Sahih. al-Dhahbi agreed with him)

2- About this 'verse' Kathir bin Salt says that he, Zaid bin Thabit and Marwan bin Hakam were discussing as to why it is not written in the Quranic manuscript and Umar bin Khattab was present with them and listening to their discussion he said he knew it better then them and told them that he came to Messenger of Allah and said:

"'O Messenger of Allah, let the verse about stoning be written for me.' He (the Prophet) said, 'I can't do this.'" (Sunan Al-Kubra Baihiqi 8/211 & Sunan Al-Kubra Nasai Hadith 7148. Albani (in Sahiha 6/412) said Baihiqi pointed to its authenticity)
Who could stop the Prophet (pbuh) from writing this verse in the Quran if it was supposed to be? Indeed it was not meant to be written in the Quran and that's why Holy Prophet disliked its idea of its being written down.

Why is it called a 'verse'?

Infact it was a verse from an earlier book as proved from Tabari's narration above and since its instruction was upheld through revelation so it is referred to as a 'verse' and the words 'sent down' or 'revealed' are used for it.

Is stoning (rajm) mentioned in the Quran today?
And as to Caliph Umar's statement 'the people may say: We do not find the punishment of stoning in the Book of Allah.', it only refers to categorical mentioning otherwise Quran does point to the punishment of stoning. Infact Quran 5:43-44 were revealed about punishment of stoning and the words 'Command of Allah' (v.43) and 'What Allah hath revealed' (v.44) refer to punishment of stoning. This becomes absolutely clear considering the traditions that Ibn Kathir, Tabari and Qurtubi etc. have brought in commentary to these verses.

And when Caliph Umar said, 'Stoning is a duty laid down in Allah's Book'he perhaps only referred to verses 43-44 of Surah 5 as mentioned above. Also we need to know that the Companions of the Prophet (pbuh) used to consider something proved from Hadith as important and as authentic as being in the Quran. The following tradition testifies to it.
'Abdullah (bin Masud) said. "Allah curses those ladies who practice tattooing and those who get themselves tattooed, and those ladies who remove the hair from their faces and those who make artificial spaces between their teeth in order to look more beautiful whereby they change Allah's creation." His saying reached a lady from Bani Asd called Um Yaqub who came (to Abdullah) and said, "I have come to know that you have cursed such-and-such (ladies)?" He replied, "Why should I not curse these whom Allah's Apostle has cursed and who are (cursed) in Allah's Book!" Um Yaqub said, "I have read the whole Quran, but I did not find in it what you say." He said, "Verily, if you have read it (i.e. the Quran), you have found it. Didn't you read: 'And whatsoever the Apostle gives you take it and whatsoever he forbids you, you abstain (from it).' (59.7). She replied, "Yes, I did," He said, "Verily, Allah's Apostle forbade such things. (Bukhari, Hadith 4507)

And as we know that punishment of stoning is clearly established in Hadith so Caliph Umar's statement can well be taken on that account.

Did Caliph Umar actually think some verse was missing?
Most certainly Caliph Umar knew well and understood that the particular words 'When a married man or woman commit adultery, stone them (to death)'are not meant to be the part of the actual text of the Holy Quran. This is clear from another tradition in which he said:

"Had it not been that people would say Umar has made an addition to the Book of Allah, I would have written it on the margin of the Quran."(Musnad Ahmad Hadith 151. Ahmad Shakir classified it as Sahih)
And according to the wording in Sunan Nasai Al-Kubra Hadith 7151 , he said 'I would have written and appended it to the Quran.'

Now idea of writing at the margin of the Quran or adding as an appendix clearly shows that he only meant to add it as side note or commentary to the Quran to tell the future generations explicitly about the punishment of stoning whom he feared rejecting this commandment and going astray.

The above detail makes it absolutely clear that never was there any verse about stoning a part of the Quranic text.

Scholars' intake:

The idea that there was never any verse on stoning revealed to be a part of the Qur'an and then abrogated is not my brainchild. Infact the above is based on Shaykh Taqi Usmani's explanation (see Takmala Fath al-Mulhim vol.2 p.354-61).

Sayyid Maududi held the same view (see his answer to the question HERE -its in Urdu)

al-Alusi quotes Ibn Humam (d. 861 A.H.) to have argued for the same (See Ruh al-M'ani 9/278)

al-Baqilani (403 A.H.) also refused to accept the idea of its once being a part of the Qur'an and then getting abrogated in his al-Intisar. Shaykh Shu'aib Arnaut quoted it in his notes to Hadith 21636 of Musnad Ahmad and seemingly agreed to it.

Moreover, this explanation puts to death all queries and questions on the issue.

The institution of Stoning (Rajm):

Regardless of the issue at hand the ruling of stoning is indeed valid. It is proved through Mutawatar Ahadith reported by around 52 companions (see Takmala Fath al-Mulhim vol.2 p.362 for all the references). The Mutawatar Ahadith decide the scope of the Qur'anic verse in Surah Nur about lashing and limit it to unmarried people. Just like Qur'an gives the general ruling that anyone who steals, man or woman, his/her hand should be amputated. The ruling is general and literally applies to a something worth a single cent even. But Mutawatir Ahadith limit it to above a certain amount.

About the narrations which say it was part of Surah Ahzab see THIS

INDEED ALLAH KNOWS THE BEST!
* the article was last updated on 4/14/2011