The fact that the Prophet Jesus (as) will rule with the Qur'an will prevent him from being recognized

Just like Muslims, Christians are also awaiting the second coming of the Prophet Jesus (as). However, when the Prophet Jesus (as) does return, he will put an end to certain corrupt beliefs and superstitions among Christians and call people to the true religious moral values revealed in the Qur’an.
All the prophets have preached the same religious moral values to the communities to which they were sent. All messengers have called on the societies in which they lived to believe in Allah alone, to serve Him, and to live the life of which He approves. They have guided their peoples in order to be saved from suffering on the Day of Judgment. Allah tells us in a verse that the faith He revealed to all the prophets and the prophets have preached to their peoples is the same religion:

He has laid down the same religion for you as He enjoined on Noah: that which We have revealed to you and which We enjoined on Abraham, Moses and Jesus…(Surat ash-Shura, 13)

Therefore, when the Prophet Jesus (as) returns to Earth he will also call people to the true faith revealed to all the prophets. That true faith is Islam. We are told that Islam is the faith in the Sight of Allah in the verse, “The religion with Allah is Islam” (Surah Al ‘Imran, 19). When he returns, the Prophet Jesus (as) will rule among people with the Qur’an, the true Holy Scripture, and by Allah’s leave, will unite all people under Islamic moral values.
Said Nursi also revealed in his own statements that Christianity would be freed from falsehood with the return of the Prophet Jesus (as) and would return to its true essence:

At that point when the current appears to be very strong, the religion of true Christianity, which comprises the collective personality of the Prophet Jesus (as), will emerge. That is, it will descend from the skies of Divine Mercy. Present Christianity will be purified in the face of that reality; it will cast off superstition and distortion, and unite with the truths of Islam. Christianity will in effect be spiritually transformed into a sort of Islam. Following the Qur’an, the collective personality of Christianity will be in the rank of follower, and Islam, in that of leader. True religion will become a mighty force as a result of its joining it. (Bediuzzaman Said Nursi, Letters / Fifteenth Letter, p. 79)

As Bediuzzaman says in these words, Christianity will be cleansed and purified from falsehood, distortions and corrupted features with the second coming of the Prophet Jesus (as). Christianity will combine with Islam, the true faith and will turn into Islam in spiritual terms.

This will be greeted with concern by those people who wish to continue with their corrupt beliefs and false practices, and may well cause the great majority of people not to recognize the Prophet Jesus (as). Believers of good conscience, who have true faith in Allah, who fear Him and know that they will give account on the Day of Judgment, will immediately believe in the Prophet Jesus (as) the moment they see him, and will follow him with all their hearts.

Our beloved Prophet Muhammad (saas) also revealed that when the Prophet Jesus (as) returns to Earth Muslims will enjoy the honor of helping this worthy individual. We are told in one hadith of our Prophet (saas) that:

... I swear by Allah Who sent me as a true prophet that (when he is sent close to the Day of Judgment) the Prophet Jesus (as), son of Mary, will find people to take the place of his disciples in my community. (Al-Hakim al-Tirmidhi, wa-manhajuhu al-Hadithi fi Nawadir al-usul, 2/92)

There is no doubt that being the Prophet Jesus’ (as) helpers is both glad tidings for genuine believers as well as a significant responsibility. It is the sincere wish of all believers to attain such an honored position as being a follower of the Prophet Jesus (as).