Abu Jafar Ar-Razi said that Ar-Rabi' bin Anas said that Abu Al-'Aliyah commented on what Allah said:

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 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:

{then kill them wherever you find them} (9:5).

However, this statement is not plausible, because Allah's statement:

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):

{...and fight against the Mushrikin collectively as they fight against you collectively} (9:36)

This is why Allah said later in the Ayah:

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:

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 'Abdul-'Aziz, Muqatil bin Hayyan and others. Muslim recorded in his Sahih that Buraydah narrated that Allah's Messenger said:

«Fight for the sake of Allah and fight those who disbelieve in Allah. Fight, but do not steal (from the captured goods), commit treachery, mutilate (the dead), or kill a child, or those who reside in houses of worship.»

It is reported in the Two Sahihs that Ibn 'Umar said, "A woman was found dead during one of the Prophet's battles and the Prophet then forbade killing women and children." There are many other Hadiths on this subject.

Shirk is worse than Killing

Since Jihad involves killing and shedding the blood of men, Allah indicated that these men are committing disbelief in Allah, associating with Him (in the worship) and hindering from His path, and this is a much greater evil and more disastrous than killing. Abu Malik commented about what Allah said:

Meaning what you (disbelievers) are committing is much worse than killing." Abu Al-'Aliyah, Mujahid, Said bin Jubayr, 'Ikrimah, Al-Hasan, Qatadah, Ad-Dahhak and Ar-Rabi' bin Anas said that what Allah said:

"Shirk (polytheism) is worse than killing."

Fighting in the Sacred Area is prohibited, except in Self-Defense

Allah said:

It is reported in the Two Sahihs that the Prophet said:

«Allah has made this city a sanctuary since the day He created the heavens and the earth. So, it is a sanctuary by Allah's decree till the Day of Resurrection. Fighting in it was made legal for me only for an hour in the daytime. So, it (i.e., Makkah) is a sanctuary, by Allah's decree, from now on until the Day of Resurrection. Its trees should not be cut, and its grass should not be uprooted. If anyone mentions the fighting in it that occurred by Allah's Messenger, then say that Allah allowed His Messenger, but did not allow you.»

In this Hadith, Allah's Messenger mentions fighting the people of Makkah when he conquered it by force, leading to some deaths among the polytheists in the area of the Khandamah. This occurred after the Prophet proclaimed:

«Whoever closed his door is safe. Whoever entered the (Sacred) Mosque is safe. Whoever entered the house of Abu Sufyan is also safe.»

Allah said:

Allah states: Do not fight them in the area of the Sacred Mosque unless they start fighting you in it. In this case, you are allowed to fight them and kill them to stop their aggression.' Hence, Allah's Messenger took the pledge from his Companions under the tree (in the area of Al-Hudaybiyyah) to fight (the polytheists), after the tribes of Quraysh and their allies, Thaqif and other groups, collaborated against the Muslims (to stop them from entering Makkah to visit the Sacred House). Then, Allah stopped the fighting before it started between them and said:

{And He it is Who has withheld their hands from you and your hands from them in the midst of Makkah, after He had made you victors over them.} (48:24)
and:

{Had there not been believing men and believing women whom you did not know, that you may kill them and on whose account a sin would have been committed by you without (your) knowledge, that Allah might bring into His mercy whom He wills - if they (the believers and the disbelievers) had been apart, We verily, would have punished those of them who disbelieved with painful torment.} (48:25)

Allah's statement:

which means, 'If they (polytheists) cease fighting you in the Sacred Area, and come to Islam and repent, then Allah will forgive them their sins, even if they had before killed Muslims in Allah's Sacred Area.' Indeed, Allah's forgiveness encompasses every sin, whatever its enormity, when the sinner repents it.

The Order to fight until there is no more Fitnah

Allah then commanded fighting the disbelievers when He said:

meaning, Shirk. This is the opinion of Ibn 'Abbas, Abu Al-'Aliyah, Mujahid, Al-Hasan, Qatadah, Ar-Rabi', Muqatil bin Hayyan, As-Suddi and Zayd bin Aslam.

Allah's statement:

means, 'So that the religion of Allah becomes dominant above all other religions.' It is reported in the Two Sahihs that Abu Musa Al-Ash'ari said: "The Prophet was asked, 'O Allah's Messenger! A man fights out of bravery, and another fights to show off, which of them fights in the cause of Allah?' The Prophet said:

«He who fights so that Allah's Word is superior, then he fights in Allah's cause.» In addition, it is reported in the Two Sahihs:

Allah's."

Under Allah's statement:

Al-Bukhari recorded that Nafi' said that two men came to Ibn 'Umar during the conflict of Ibn Az-Zubayr and said to him, "The people have fallen into shortcomings and you are the son of 'Umar and the Prophet's Companion. Hence, what prevents you from going out?" He said, "What prevents me is that Allah has forbidden shedding the blood of my (Muslim) brother." They said, "Did not Allah say:

{And fight them until there is no more Fitnah (disbelief and worshipping of others along with Allah)}?"

He said, "We did fight until there was no more Fitnah and the religion became for Allah Alone. You want to fight until there is Fitnah and the religion becomes for other than Allah!"

'Uthman bin Salih added that a man came to Ibn 'Umar and asked him, "O Abu 'Abdur-Rahman! What made you perform Hajj one year and 'Umrah another year and abandon Jihad in the cause of Allah, although you know how much He has encouraged performing it?" He said, "O my nephew! Islam is built on five (pillars): believing in Allah and His Messenger, the five daily prayers, fasting Ramadan, paying the Zakah and performing Hajj (pilgrimage) to the House." They said, "O Abu 'Abdur-Rahman! Did you not hear what Allah said in His Book:

{And if two parties (or groups) among the believers fall to fighting, then make peace between them both. But if one of them outrages against the other, then fight you (all) against the one that which outrages till it complies with the command of Allah.} (49:9) and:

{And fight them until there is no more Fitnah (disbelief)}?"

He said, "That we did during the time of Allah's Messenger when Islam was still weak and (the Muslim) man used to face trials in his religion, such as killing or torture. When Islam became stronger (and apparent), there was no more Fitnah." He asked, "What do you say about 'Ali and 'Uthman?" He said, "As for 'Uthman, Allah has forgiven him. However, you hated the fact that Allah had forgiven him! As for 'Ali, he is the cousin of Allah's Messenger and his son-in-law." He then pointed with his hand, saying, "This is where his house is located (meaning, 'so close to the Prophet's house just as 'Ali was so close to the Prophet himself)."