The verse in the Qur’an you are referring to is:
004.157 وَقَوْلِهِمْ إِنَّا قَتَلْنَا الْمَسِيحَ عِيسَى ابْنَ مَرْيَمَ رَسُولَ اللَّهِ وَمَا قَتَلُوهُ وَمَا صَلَبُوهُ وَلَكِنْ شُبِّهَ لَهُمْ وَإِنَّ الَّذِينَ اخْتَلَفُوا فِيهِ لَفِي شَكٍّ مِنْهُ مَا لَهُمْ بِهِ مِنْ عِلْمٍ إِلا اتِّبَاعَ الظَّنِّ وَمَا قَتَلُوهُ يَقِينًا
004.157 That they said (in boast), “We killed Christ Jesus the son of Mary, the Messenger of Allah”;- but they killed him not, nor crucified him, but so it was made to appear to them, and those who differ therein are full of doubts, with no (certain) knowledge, but only conjecture to follow, for of a surety they killed him not:- Al-Qur’an, 004.157 (An-Nisa [Women]).
A-002.087 وَلَقَدْ آتَيْنَا مُوسَى الْكِتَابَ وَقَفَّيْنَا مِنْ بَعْدِهِ بِالرُّسُلِ وَآتَيْنَا عِيسَى ابْنَ مَرْيَمَ الْبَيِّنَاتِ وَأَيَّدْنَاهُ بِرُوحِ الْقُدُسِ أَفَكُلَّمَا جَاءَكُمْ رَسُولٌ بِمَا لا تَهْوَى أَنْفُسُكُمُ اسْتَكْبَرْتُمْ فَفَرِيقًا كَذَّبْتُمْ وَفَرِيقًا تَقْتُلُونَ
002.087 We gave Moses the Book and followed him up with a succession of messengers; We gave Jesus the son of Mary Clear (Signs) and strengthened him with the holy spirit. Is it that whenever there comes to you a messenger with what ye yourselves desire not, ye are puffed up with pride?- Some ye called impostors, and others ye slay! Al-Qur’an, 002.087 (Al-Baqara [The Cow])
B- 003.055 إِذْ قَالَ اللَّهُ يَا عِيسَى إِنِّي مُتَوَفِّيكَ وَرَافِعُكَ إِلَيَّ وَمُطَهِّرُكَ مِنَ الَّذِينَ كَفَرُوا وَجَاعِلُ الَّذِينَ اتَّبَعُوكَ فَوْقَ الَّذِينَ كَفَرُوا إِلَى يَوْمِ الْقِيَامَةِ ثُمَّ إِلَيَّ مَرْجِعُكُمْ فَأَحْكُمُ بَيْنَكُمْ فِيمَا كُنْتُمْ فِيهِ تَخْتَلِفُونَ
003.055 Behold! Allah said: “O Jesus! I will take thee* and raise thee to Myself and clear thee (of the falsehoods) of those who blaspheme; I will make those who follow thee superior to those who reject faith, to the Day of Resurrection: Then shall ye all return unto me, and I will judge between you of the matters wherein ye dispute. Al-Qur’an, 003.055 (Aal-E-Imran [The Family of Imran])
* “take thee” in Arabic means “cause my death” (مُتَوَفِّيكَ).
C- 005.117 مَا قُلْتُ لَهُمْ إِلا مَا أَمَرْتَنِي بِهِ أَنِ اعْبُدُوا اللَّهَ رَبِّي وَرَبَّكُمْ وَكُنْتُ عَلَيْهِمْ شَهِيدًا مَا دُمْتُ فِيهِمْ فَلَمَّا تَوَفَّيْتَنِي كُنْتَ أَنْتَ الرَّقِيبَ عَلَيْهِمْ وَأَنْتَ عَلَى كُلِّ شَيْءٍ شَهِيدٌ
005.117 “Never said I to them aught except what Thou didst command me to say, to wit, ‘worship Allah, my Lord and your Lord’; and I was a witness over them whilst I dwelt amongst them; when Thou didst take me* up Thou wast the Watcher over them, and Thou art a witness to all things. Al-Qur’an, 005.117 (Al-Maeda [The Table, The Table Spread])
* “take thee” in Arabic means “cause my death” (تَوَفَّيْتَنِي).
D- 019.033 وَالسَّلامُ عَلَيَّ يَوْمَ وُلِدْتُ وَيَوْمَ أَمُوتُ وَيَوْمَ أُبْعَثُ حَيًّا
019.033 “So peace is on me the day I was born, the day that I die, and the day that I shall be raised up to life (again)”!
019.034 ذَلِكَ عِيسَى ابْنُ مَرْيَمَ قَوْلَ الْحَقِّ الَّذِي فِيهِ يَمْتَرُونَ
019.034 Such (was) Jesus the son of Mary: (it is) a statement of truth, about which they (vainly) dispute.Al-Qur’an, 019.033-034 (Maryam [Mary]).
Second- The first verse simply, means that the Jews thought that by allowing the Romans to kill Jesus they were able to succeed in their plans to silence and destroy Him forever. But what appeared to them was not what really took place. The picture of this success was temporary. For God Almighty raised Him up again and took Him to heaven and gave Him victory over the devil.
In His service,
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