Praise be to Allah.

Firstly: 

No nation, apart from the ummah of Islam, can soundly prove the chain of narrators of its stories and their history going back to their Prophet. That is because Allah, may He be exalted, did not guarantee to preserve the books of other religions that came before the Qur’an, and there is no other nation that paid attention to the chains of narrators before the ummah of Islam. Therefore, all that they narrated of events and stories from their Prophets and their earlier history comes under the heading of that which cannot be proven, so their religious teachings were exposed to distortions, fabrications and lies. As for the ummah of Islam, Allah, may He be exalted, told them of some of the stories of those who came before them of other nations, and of some of the stories of the previous Prophets and messengers; these are true stories, but there is nothing contrary to them except fabrications and lies. 

One of the stories of the unseen for which we have proof, but concerning which there were different views among other nations, is what happened to the Prophet of Allah ‘Eesaa. Allah, may He be exalted, has told us that he was not killed or crucified, and that He, may He be exalted, caused someone else to resemble him, and it was this other person whom they killed and crucified, not ‘Eesaa (peace be upon him). Our Lord, may He be exalted, has told us that He took him up to Him, and that he will descend at the end of time, when he will kill the pigs, break the cross and rule according to Islam. As for others who claim to be his followers, they differed greatly concerning him. Some of them said that he was God, and some said that he was the son of God! Those who saw ‘Eesaa (peace be upon him) being taken up and saw the other person being caused to resemble him were very few, and they are the ones who did not believe that he was anything more than a Prophet and Messenger. 

Ibn Katheer (may Allah have mercy on him) said in Tafseer Ibn Katheer (2/47): When Allah took the Messiah (peace be upon him) up to heaven, his followers split into sects after he was gone. Some of them believed in that with which Allah had sent him, and believed that he was a slave of Allah, His Messenger and the son of His female slave. Some of them exaggerated about him and regarded him as the son of God, and others even said that he was God. Others said that he was the third of three. Allah has told us of what they said in the Qur’an, and He refuted each group.

End quote. 

Secondly: 

The belief of Ahl as-Sunnah wa’l-Jamaa‘ah is that the Messiah ‘Eesaa (peace be upon him) was not crucified or killed. The source of this belief is the clear texts of the Qur’an, and none of the Muslims disagrees with that. Whoever disagrees with that is an apostate. 

The Scholars of the Standing Committee were asked: 

Is ‘Eesaa ibn Maryam alive or dead? What is the evidence from the Qur’an or Sunnah? If he is alive or dead, then where is he now? And what is the evidence for that from the Qur’an and Sunnah? 

They replied: 

‘Eesaa ibn Maryam (blessings and peace of Allah be upon him) is alive; he has not died up till now. The Jews did not kill him or crucify him; rather it was caused to appear that way to them. Allah took him up to heaven, body and soul, and until now he is in heaven. The evidence for that is the words of Allah, may He be exalted, concerning the fabrication of the Jews and the refutation thereof (interpretation of the meaning):

“And because of their saying (in boast), "We killed Messiah ‘Eesaa (Jesus), son of Maryam (Mary), the Messenger of Allah," - but they killed him not, nor crucified him, but the resemblance of ‘Eesaa (Jesus) was put over another man (and they killed that man), and those who differ therein are full of doubts. They have no (certain) knowledge, they follow nothing but conjecture. For surely; they killed him not (i.e. ‘Eesaa (Jesus), son of Maryam (Mary) )

But Allah raised him (‘Eesaa (Jesus)) up (with his body and soul) unto Himself (and he is in the heavens). And Allah is Ever All-Powerful, All-Wise”

[an-NIsa’ 4:157-158]. 

Thus Allah, may He be glorified, declared false the words of the Jews when they claimed that they had killed him and crucified him, and He stated that He took him up to Him. That was mercy from Him to him, and was an honour to him, so that he would be one of his signs, an honour that He bestows upon whomever He will of His Messengers. How many signs of Allah there are in the story of ‘Eesaa ibn Maryam (peace be upon him), from beginning to end. The implication of the words “But Allah raised him (‘Eesaa (Jesus)) up (with his body and soul) unto Himself” is that Allah, may He be glorified, took ‘Eesaa (blessings and peace of Allah be upon him) up body and soul, so as to refute the claim of the Jews that they crucified him and killed him, because killing and crucifying have to do with the physical body. Moreover, if He had only taken up his soul, that would not rule out the claim of having killed and crucified him, because taking up the soul only would not be a refutation of their claim. Also the name of ‘Eesaa (peace be upon him), in reality, refer to him in both soul and body together; it cannot refer to one of them only, unless there is an indication to that effect. Furthermore, taking up both his soul and his body together is indicative of the perfect might and wisdom of Allah, and of His honour and support to whomever He will among His Messengers, according to what He, may He be exalted, says at the end of the verse: “And Allah is Ever All-Powerful, All-Wise.” 

Shaykh ‘Abd al-‘Azeez ibn Baaz, Shaykh ‘Abd ar-Razzaaq ‘Afeefi, Shaykh ‘Abdullah ibn Ghadyaan, Shaykh ‘Abdullah ibn Qa‘ood. 

End quote from Fataawa al-Lajnah ad-Daa’imah (3/305-306) 

For more details, please see ibid. (3/299-305) 

For more information on the Muslim belief in the Messiah (peace be upon him), please see the answer to question no. 43148 

In the answer to question no. 10277 you will find a brief discussion on the Prophet of Allah ‘Eesaa (peace be upon him). 

In the answer to question no. 12615 you will find a discussion with a Christian on the (alleged) crucifixion of the Messiah. 

In the answer to question no. 43506 you will find a response to questions about the verses that speak of the life and death of the Messiah (peace be upon him). 

Thirdly: 

With regard to the grave of the Messiah and his emergence therefrom, and the similarity of that sign to the sign of Jonah (Yoonus – peace be upon him), these issues have been discussed by our specialist scholars, who explained how this is misguided and contradictory; they have explained how misguided and flawed this story is. 

Al-Hindi (may Allah have mercy on him) said, commenting on the passage referred to in the question: 

The scribes and Pharisees demanded a miracle, but ‘Eesaa (peace be upon him) did not give them a miracle at that time, and did not refer to them to miracle that he had performed before they made their demand; rather he reviled them and called them wicked and evil, and he promised a miracle that he had not yet performed, because the statement “As Jonah was in the belly of the fish…” undoubtedly cannot be attributed to him, as explained in the third section of the first chapter. 

If we ignore the fact that this statement cannot be attributed to him, then the scribes and Pharisees did not see his (supposed) resurrection with their own eyes. If ‘Eesaa (peace be upon him) did indeed rise from the dead, he should have shown himself to these doubters who demanded a sign, so as to establish proof against them and fulfil his promise. But he did not show himself to them or to the other Jews, not even once, therefore they do not believe in this resurrection; rather what they say, since that time and up until the present, is that his disciples stole his body from the grave at night. 

Izhaar al-Haq (4/1214) 

Shaykh Ahmad Deedat (may Allah have mercy on him) wrote three books about the same topic. They are: What Was the Sign of Jonah?, Resurrection or Resuscitation?, and Who Moved the Stone?  

There is no value at all in their texts, because they have been altered and distorted, and they contain fabrications and falsehood. Moreover, scholars have highlighted their flaws. 

Finally: 

We advise the questioner, and others who read these words, to focus on the teachings of his own religion and on obeying his Lord, may He be exalted, and to refrain from seeking out the misguidance of other sects and religions. That battle has its own knights, and there is no reason why he should not be one of them, but this requires academic experience and lengthy pursuit of knowledge, as well as knowing the truth with evidence to support it. We ask Allah, may He be exalted, to guide the Muslims to that which is best for their religious and worldly interests. 

And Allah knows best.