وَٱقْتُلُوهُمْ حَيْثُ ثَقِفْتُمُوهُمْ وَأَخْرِجُوهُم مِّنْ حَيْثُ أَخْرَجُوكُمْ ۚ وَٱلْفِتْنَةُ أَشَدُّ مِنَ ٱلْقَتْلِ ۚ وَلَا تُقَٰتِلُوهُمْ عِندَ ٱلْمَسْجِدِ ٱلْحَرَامِ حَتَّىٰ يُقَٰتِلُوكُمْ فِيهِ ۖ فَإِن قَٰتَلُوكُمْ فَٱقْتُلُوهُمْ ۗ كَذَٰلِكَ جَزَآءُ ٱلْكَٰفِرِينَ
And kill them wherever you overtake them and expel them from wherever they have expelled you, and fitnah is worse than killing. And do not fight them at al-Masjid al- Haram until they fight you there. But if they fight you, then kill them. Such is the recompense of the disbelievers.
And fight in the way of Allah those who fight you, but transgress not the limits. Truly, Allah likes not the transgressors (190)And kill them wherever you find them, and turn them out from where they have turned you out. And Al-Fitnah is worse than killing. And fight not with them at Al-Masjid Al-Haram (the sanctuary at Makkah), unless they (first) fight you there. But if they attack you, then kill them. Such is the recompense of the disbelievers (191)But if they cease, then Allah is Oft-Forgiving, Most Merciful (192)And fight them until there is no more Fitnah (disbelief and worshipping of others along with Allah) and the religion (all and every kind of worship) is for Allah (Alone). But if they cease, let there be no transgression except against Az-Zalimin (the polytheists and wrongdoers)(193)
The Command to fight Those Who fight Muslims and killing Them wherever They are found
Abu Ja'far Ar-Razi said that Ar-Rabi' bin Anas said that Abu Al-'Aliyah commented on what Allah said:
وَقَاتِلُوا فِي سَبِيلِ اللَّهِ الَّذِينَ يُقَاتِلُونَكُمْ
(And fight in the way of Allah those who fight you,)
Abu Al-'Aliyah said, "This was the first Ayah about fighting that was revealed in Al-Madinah. Ever since it was revealed, Allah's Messenger ﷺ used to fight only those who fought him and avoid non-combatants. Later, Surat Bara'ah (chapter 9 in the Qur'an) was revealed." 'Abdur-Rahman bin Zayd bin Aslam said similarly, then he said that this was later abrogated by the Ayah:
فَاقْتُلُوا الْمُشْرِكِينَ حَيْثُ وَجَدتُّمُوهُمْ
(then kill them wherever you find them)(9:5).
However, this statement is not plausible, because Allah's statement:
الَّذِينَ يُقَاتِلُونَكُمْ
(...those who fight you) applies only to fighting the enemies who are engaged in fighting Islam and its people. So the Ayah means, 'Fight those who fight you', just as Allah said (in another Ayah):
وَقَاتِلُوا الْمُشْرِكِينَ كَافَّةً كَمَا يُقَاتِلُونَكُمْ كَافَّةً
(...and fight against the Mushrikin collectively as they fight against you collectively.)(9:36)
This is why Allah said later in the Ayah:
وَاقْتُلُوهُمْ حَيْثُ ثَقِفْتُمُوهُمْ وَأَخْرِجُوهُم مِّنْ حَيْثُ أَخْرَجُوكُمْ
(And kill them wherever you find them, and turn them out from where they have turned you out.) meaning, 'Your energy should be spent on fighting them, just as their energy is spent on fighting you, and on expelling them from the areas from which they have expelled you, as a law of equality in punishment.'
The Prohibition of mutilating the Dead and stealing from the captured Goods
Allah said:
وَلَا تَعْتَدُوا إِنَّ اللَّهَ لَا يُحِبُّ الْمُعْتَدِينَ
(but transgress not the limits. Truly, Allah likes not the transgressors.)
This Ayah means, 'Fight for the sake of Allah and do not be transgressors,' such as, by committing prohibitions. Al-Hasan Al-Basri stated that transgression (indicated by the Ayah), "includes mutilating the dead, theft (from the captured goods), killing women, children and old people who do not participate in warfare, killing priests and residents of houses of worship, burning down trees and killing animals without real benefit." This is also the opinion of Ibn 'Abbas, 'Umar bin …