As-salaamu 'alaikum!
Context is the key
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Chapter 9
9:1 A revocation is made by God and His messenger to those with whom you have made a pledge from among the polytheists.
9:2 "Therefore,
roam the land for four months and know that you will not escape God, and that God will humiliate the rejecters."
9:3 And a proclamation from God and His messenger to the people, on the day of the greater Pilgrimage:
"That God and His messenger are innocent from the polytheists." If you repent, then it is better for you, and if you turn away, then know that you will not escape God. And give news to those who have rejected of a painful retribution.
9:4
Except for those with whom you had made a pledge from among the polytheists if they did not reduce anything from it nor did they support anyone against you; you shall continue the pledge with them until its expiry. God loves the righteous.9:5
So when the restricted months have passed (Four months mentioned in 9:2),
then you may kill the polytheists wherever you find them, and take them, and surround them, and stand against them at every point. If they repent, and they hold the contact prayer, and they contribute towards purification, then you shall leave them alone. God is Forgiving, Merciful. (For those polytheists who broke/turned away from their oaths/pledges. The other polytheists that did not break the pledges/oaths were not harmed in anyway)9:6
And if any of the polytheists seeks your protection, then you may protect him so that he may hear the words of God, then let him reach his sanctity. This is because they are a people who do not know.9:7 How can the polytheists have a pledge with God and with His messenger?
Except for those with whom you made a pledge near the Restricted Temple, as long as they are upright with you, then you are upright with them. God loves the righteous.
9:8
How is it that when they come upon you they disregard all ties, either those of kinship or of pledge. They seek to please you with their words, but their hearts deny, and the majority of them are wicked.
9:9
They purchased with the revelations of God a cheap price, so they repel others from His path. Evil indeed is what they used to do.
9:10
They do not respect those who are believers, nor a kinship, nor a pledge. These are the transgressors.
9:11 If they repent, and they hold the contact prayer, and they contribute towards purification, then they are your brothers in the system. We explain the revelations for a people who know.
9:12
And if they break their oaths after making their pledge, and they challenge the authority of your system; then you may kill the leaders of rejection. Their oaths are nothing to them, perhaps they will then cease.
9:13
Would you not fight a people who broke their oaths, and obsessed to expel the messenger, especially while they were the ones who attacked you first? Are you concerned about them? It is God who is more deserving that you be concerned with if you are believers.
9:14 Fight them; perhaps God will punish them by your hands and humiliate them and grant you victory over them and heal the chests of the believing people.
9:15 And to remove the anger from their hearts; God pardons whom he pleases. God is Knowledgeable, Wise.
9:16 Or did you think that you would be left alone? God will come to distinguish those of you who strived and did not take other than God and His messenger and the believers as helpers. God is Expert in what you do.
9:17 It was not for the polytheists to maintain the temples of God while they bear witness over their own rejection. For these, their works have fallen, and in the Fire they will abide.
9:18 Rather, the temples of God are maintained by he who believes in God and the Last Day, and he upholds the contact prayer, and he contributes towards purification, and is only concerned by God. It is these that will be of the guided ones.
9:19 Have you made the watering of the pilgrim and the maintenance of the Restricted Temple the same as one who believes in God and the Last Day and he strives in the cause of God? They are not the same with God. And God does not guide the wicked people.
9:20 Those who believed and emigrated and strived in the cause of God with their money and their lives are in a greater degree with God. These are the winners.
9:21 Their Lord gives them good news of a mercy from Him, and acceptance, and gardens that are for them in which there is permanent bliss.
9:22 They will abide in it eternally. With God there is a great reward.
9:23 O you who believe, do not take your fathers nor brothers as allies if they prefer rejection to belief. And whoever of you takes them as such, then these are the wicked.
9:24 Say: "If your fathers, and your sons, and your brothers, and your wives, and your kin, and money which you have gathered, and a trade which you would be concerned over its decline, and homes which you find pleasing; if these are dearer to you than God and His messenger and striving in His cause, then wait until God brings His decision. And God does not guide the wicked people."
9:25 God has granted you victory in many battlefields. And on the day of Hunayn when you were pleased with your great numbers but it did not help you at all, and the land became tight around you for what it held, then you turned to flee.
9:26 Then God sent down His tranquility upon His messenger and the believers, and He sent down soldiers which you did not see, and He punished those who rejected. Such is the recompense of the rejecters.
9:27 Then God will accept the repentance of whom He pleases after that. God is Forgiving, Merciful.
9:28 O you who believe, the polytheists are impure, so let them not approach the Restricted Temple after this common year of theirs; and if you fear poverty, then God will enrich you from His blessings if He wills. God is Knowledgeable, Wise.
9:29 Fight those who do not believe in God or the Last Day, nor do they forbid what God and His messenger have forbidden, nor do they uphold the system of truth; from among the people who have been given the Book; until they pay the reparation, willingly or unwillingly, and they are subdued.
9:30 The Jews said: "Ezra is the son of God," and the Nazarenes said: "The Messiah is the son of God." Such is their utterances with their mouths, they imitate the sayings of those who rejected before them. God will fight them. They are deluded from the truth!
9:31 They have taken their Priests and Monks to be patrons besides God, and the Messiah, son of Mary, while they were only commanded to serve One god, there is no god except He, be He glorified against what they set up.
9:32 They want to extinguish the light of God with their mouths, but God refuses such and lets His light continue, even if the rejecters hate it.
I don't understand what problems the Muslims has with these verses of the Qur'aan! I've no problem and context is very important!
Regards,
Ijaz, A.