The following is stated in verse 5 of the chapter of at-Tawba: "…slay the pagans wherever ye find them…" Will you explain this verse?

Details of the Question
The following is stated in verse 5 of the chapter of at-Tawba: "…slay the pagans wherever ye find them…" Will you explain this verse?
The Answer

Dear Brother / Sister,

"But when the forbidden months are past, then fight and slay the pagans wherever ye find them, and seize them, beleaguer them, and lie in wait for them in every stratagem (of war); but if they repent, and establish regular prayers and practice regular charity, then open the way for them: for Allah is Oft-Forgiving, Most Merciful." (at-Tawba, 9/5)

The verse above orders Muslims to fight the idolaters of that time. However, if any group attacks the community of Islam today, it becomes fard for the Muslims of that region to fight the unbelievers that attack them.

"Killing" will be used as the last resort for the measures mentioned in the verse to be consistent. For, if killing is resorted to first, the other measures become meaningless. Killing the enemy is one of the natural outcomes of war; so, the reason why killing (slaying) is mentioned in the verse probably aims to remind Muslims not to resort to it before taking the other measures. As a matter of fact, if the idolaters repent but do not accept Islam at once, the Muslims are asked to give them security and the opportunity to learn Islam from Muslims by living among them and to think about Islam in the verse.  This understanding is more appropriate to the other statements of the Quran regarding killing.

After the forbidden months, the state of war started between you and them. Then, declare war on them without waiting for their attack; kill them wherever you find them and however you can.
 
However, the believers are forbidden from committing muthla; that is, cutting off the organs of a person like the nose or ear, to stop a person, to tie his hands and arms and to kill him with an arrow or a similar tool by torturing him. The Prophet (pbuh) stated the following regarding the issue:

"The most merciful people in terms of killing are believers." He also said,
"When you kill, kill in a nice way." Those verses also imply that it is necessary to do so:

"And seize them, beleaguer them." That is, if it is possible to seize them and to beleaguer them, do not attempt to kill them. Put them on probation; do not allow them to go wherever they want; "lie in wait for them in every stratagem of war"; that is, lie in wait on ways of trade, expedition, etc and watch them. It was necessary to take all kinds of measures in order to purify the Kaaba from the existence and domination of idolaters. (Kuran Yolu, Diyanet, the interpretation of the relevant verse)

"If they repent, that is, if they abandon idolatry and become believers, and establish regular prayers and practice regular charity, that is, if they become Muslims by accepting to perform prayers and give zakah, then open the way for them; do not do any of the things mentioned above to them. Leave them free. For, Allah is Oft-Forgiving, Most Merciful. He forgives what they committed before, their idolatry, unbelief and injustice because they become believers and gives them rewards for their belief and worshipping.   

That is, those idolaters are given the following alternatives: death, slavery or becoming Muslims. As it will be mentioned later, jizyah will not be accepted from them unlike the People of the Book. Hasan al-Basri narrates the following: One of the slaves of war uttered the following in a way that the Prophet (pbuh) would hear three times: 'I will repent to Allah; I will not repent to Muhammad.' The Prophet (pbuh) said, 'Leave him; he gave the One His due.'"(Elmalılı Hamdi Yazır, the interpretation of the relevant verse)

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