Till the time Islam was weak during the Meccan period and the initial Medinan period, Quranic verses taught peace and tolerance and justice. But as soon as Islam became stronger in the later Medinan period, then it started teaching violence, cruelty, coercion, and intolerance.

Let us compare Quranic Verses during these 2 periods to see these double standards of the Quran.

 

Meccan and Initial Medinan Period, when Islam was weak

Later Medinan Period, when Islam became stronger

1

For you is your religion, and for me is my religion." (109.6)

And whoever desires other than Islam as religion - never will it be accepted from him, and he, in the Hereafter, will be among the losers. (3:85)

2

And be patient over what they say and avoid them with gracious avoidance. (73.10)

I will cast terror into the hearts of those who disbelieved, so strike [them] upon the necks and strike from them every fingertip. (8.12)

3

There shall be no compulsion in [acceptance of] the religion. (2:256)

O you who have believed, fight those adjacent to you of the disbelievers and let them find in you harshness. (9:123)

4

And speak to people good [words] (2;83)

kill the polytheists wherever you find them and capture them and besiege them and sit in wait for them at every place of ambush.(9:5)

5

And had your Lord willed, those on earth would have believed - all of them entirely. Then, [O Muhammad], would you compel the people in order that they become believers?(10:99)

Fight them until there is no [more] fitnah and [until] worship is [acknowledged to be] for Allah (2:193)

6

We know best what they say; and thou art not one to overawe them by force. (50:45)

Fight them; Allah will punish them by your hands and will disgrace them and give you victory over them and satisfy the breasts of a believing people (9.14)

7

And do not argue with the People of the Scripture except in a way that is best,  (29:46)

Fight against such of those who have been given the Scripture as believe not in Allah nor the Last Day, and forbid not that which Allah hath forbidden by His messenger, and follow not the Religion of Truth, until they pay the tribute readily, being brought low. (9:29)

8

Those who believe, and those who follow the Jewish (scriptures), and the Christians and the Sabians,- any who believe in Allah and the Last Day, and work righteousness, shall have their reward with their Lord; on them shall be no fear, nor shall they grieve. (2:62)

The Jews say, "Ezra is the son of Allah "; and the Christians say, "The Messiah is the son of Allah." That is their statement from their mouths; they imitate the saying of those who disbelieved [before them]. May Allah destroy them; how are they deluded? (9:30)

9

Keep to forgiveness (O Muhammad), and enjoin kindness, and turn away from the ignorant. (7:199)

O you who have believed, indeed the polytheists are unclean, so let them not approach al-Masjid al-Haram (9:28)

10

So overlook (any human faults of Non-Muslims) with gracious forgiveness. (15:85)

He will gulp it but will hardly [be able to] swallow it. And death will come to him from everywhere, but he is not to die. And before him is a massive punishment. (14:17)

11

And do not insult those they invoke other than Allah (6:108)

Then whoever argues with you about it after [this] knowledge has come to you - say, "Come, let us call our sons and your sons, our women and your women, ourselves and yourselves, then supplicate earnestly [together] and invoke the curse of Allah upon the liars [among us]." (3.61)

12

(If they don’t believe in you, O Muhammad) So turn aside from them and say, "Peace." (43:89)

So when you meet those who disbelieve, strike [their] necks (47:4)

13

and thou (O Muhammad) art not one to overawe them by force. (50:45)

O Prophet! Exhort the believers to fight. (8.65)

14

Indeed, Allah orders justice and good conduct and giving to relatives (Muslim and non-Muslim relatives alike) and forbids immorality and bad conduct and oppression. (16:90)

Let not the believers take disbelievers for their friends in preference to believers. Whoso doeth that hath no connection with Allah (3:28)

15

Tell [O Muhammad], those who believe, to forgive those who do not look forward to the Days of Allah (i.e. Non-Muslims): It is for Him to recompense (for good or ill) each People according to what they have earned. (45:14)

Against them make ready your strength to the utmost of your power, including steeds of war, to strike terror into (the hearts of) the enemies (8.60)

 

In the 9th Hijri year, Muhammad got “absolute power” and no one was left there in the entire Arabia who could have opposed him. Thus, then in the 9th Hijri year, Muhammad claimed the revelation of verse 9:5 and made the killing of all polytheists Halal (permissible) for Muslims after 4 months (or after the expiration date for those Arab tribes, who made the treaties with Muhammad after the victory of Mecca).

Quran 9:5:

(After 4 months) kill all the polytheists wherever you find them and capture them and besiege them and sit in wait for them at every place of ambush.

And the Quranic verse 9:29 again testifies the same thing that the order of killing all polytheists was not due to the reason that they were fighting Muslims, but it was due to the reason that they didn’t believe in Allah and Muhammad.

(Quran 9:29) Fight those people of the Book (Jews and Christians) who do not believe in Allah and the Last Day, do not refrain from what has been prohibited by Allah and His Messenger and do not embrace the religion of truth (Al-Islam), until they pay Jizya (protection tax) with their own hands and feel themselves subdued.

Note: This verse also allows Jizya from only the “People of the Book” (i.e. Jews and Christians and Zoroastrians), while polytheists were not even allowed to live after paying the Jizya. Polytheists either had to accept Islam, or they would be killed after 4 months (or till the end of their covenant). 

And then there are traditions which are clear about how Muslims killed even peaceful polytheists after the revelation of this verse:

Sahih Bukhari, Book of Battles (link):

Narrated Jarir: In the Pre-lslamic Period of Ignorance there was a house called Dhu-l-Khalasa or Al-Ka'ba Al-Yamaniya or Al-Ka'ba Ash-Shamiya. The Prophet said to me, "Won't you relieve me from Dhu-l-Khalasa?" So I set out with one-hundred-and-fifty riders, and we dismantled it and killed whoever was present there. Then I came to the Prophet and informed him, and he invoked good upon us and Al-Ahmas (tribe) .

Musanif Ibn Abi Shaybah, 6/586, Kitab-ul-Hadood, chapter of في الزنادقة ما حدهم (link):

Some people used to worship their idols secretly. They were arrested and brought to 4th caliph Ali Ibn Abi Talib. He consulted the people how to punish them. People suggested to kill them. Ali said: No, I will not simply kill them, but I will do that act which was performed by them against my ancestor Abraham. After that Ali burnt all of them in the fire.

And when Umar Ibn Khattab conquered Persia, he used this same verse 9:5 as an argument to kill them, and all the Sahaba (companions) stayed quiet upon it and no one opposed Umar Ibn Khattab by telling him that this verse was limited to Polytheist of Mecca or Arabia only. Therefore, there was an IJMA (unanimous decision) by Sahaba upon this verse, it orders the killing of all the Polytheists.

But then Umar Ibn Khattab didn’t kill the Persians while Ali and 'Abd al-Rahman ibn 'Awf told him that Zoroastrians of Persia were also counted as “People of the Book” by Prophet Muhammad. Thus, he took Jazya from them, and then he let them live.

Imam Ibn Hajr al-Asqallani recorded this Sahih (authentic) tradition (link):

وروى عبد بن حميد في تفسير سورة البروج بإسناد صحيح عن ابن أبزى " لما هزم المسلمون أهل فارس قال عمر : اجتمعوا . فقال : إن المجوس ليسوا أهل كتاب فنضع عليهم ، ولا من عبدة الأوثان فنجري عليهم أحكامهم فقال علي : بل هم أهل كتاب "’
Translation:
When Muslims defeated the Persians, then Umar Ibn Khattab asked Sahaba (companions) to gather and to tell him what to do with the Persians as they are neither from the “People of Book” that they could take Jizya from them, and nor were they the polytheists that they should all be killed. Upon that Ali Ibn Abi Talib told him that Zoroastrians were also counted as “People of the Book”.

Thus, the Persians escaped the slaughter while they were also counted as the “People of the Book”, otherwise they would have also been killed as polytheists.

This shows that the order of killing the polytheists was neither limited to the era of Muhammad (but this order stays true even after his death), nor it was limited to only Arabia, but to the whole world. And it was also not limited to the battlefield, while the Persians had already been defeated, and had already surrendered, but still, Umar Ibn Khattab wanted to kill them all had they not accepted Islam. 

And now look at this “authentic” tradition of Sunan Abu Dawud (link):

لم يكن عمر يأخذ الجزية من المجوس حتى شهد عبد الرحمن بن عوف أن رسول الله صلى الله عليه وسلم أخذها من مجوس هجر .
Translation:
Umar Ibn Khattab didn’t want to take Jizya (but wanted to kill them all), but 'Abd al-Rahman ibn 'Awf told him that Prophet Muhammad took Jizya from the Zoroastrians of the place of Hijr.

Imam Shafii, Imam Ahmed bin Hanbal, and Imam Ibn Hazam all said that all polytheists of the entire world should be killed according to this verse 9:5, and no Jizya can be taken from them, and they have only one choice to save their life i.e. to accept Islam.

While Abu Hanifa limited this order only to the polytheists of Arabia, while the non-Arab polytheists could pay Jizya and stay alive according to him. Nevertheless, Abu Hanifa went against the Ijm'a of Sahaba, where Umar Ibn Khattab wanted to kill the non-Arab Persians due to this verse, and all Sahaba agreed with him (but Persians escaped this genocide while it was proved that they were also from the People of the Book). 

Thus, Imam Shafii and Imam Ahmed bin Hanbal rejected the opinion of Abu Hanfia, by using the Ijma (unanimous decision) of Sahaba, where none of them rejected the opinion of Umar that all polytheists should be killed.

Shafii and Hanbali Scholars used the decision of Umar Ibn Khattab that only the “people of the Book” are allowed to live after paying Jizya. Umar was in doubt if Zoroastrians of Persian were included in “people of book” or not. Thus, had it been proved upon him that they were not from the “people of the book”, then he would have compelled them to accept Islam like the polytheists, and if they had rejected to accept Islam, then he would have killed them all.
References:
(1) Imam Shafii, Kitab al-Am, vol. 4, page 174
(2) Ibn Qadammah Hanbali, Book al-Mughani, vol. 9, page 173

PS: 
The Muslim Sultans, who conquered India, took Jizya from Hindus too and didn't kill them. It was due to the reason that they were the followers of Hanafi Fiqh, and Imam Abu Hanifa allowed them to take Jizya from the non-Arab polytheists. This saved the Hindus from being slaughtered. 

Present-day Salafis still consider that all polytheists of the whole world should be killed according to the order of this verse 9:5.

Saudi Grand Mufti Ibn Baaz wrote (link):

، والأرجح أنه لا يلحق بهم غيرهم ، بل هؤلاء الطوائف الثلاث هم الذين يخيرون ؛ لأن الرسول قاتل الكفار في الجزيرة ولم يقبل منهم إلا الإسلام ،
Translation:
And the correct view is this that polytheists (of today) do not come under the category of “people of the book”, but only Jews, Christians and Zoroastrians are allowed to live by paying Jizya, while Prophet Muhammad killed all the polytheists in Arabia and accepted nothing from them, except Islam.

That is why ISIS allowed the Christians of Iraq to pay Jizya and didn’t kill them. But ISIS didn’t accept any Jizya from the Yazidi community of Iraq, and they killed the Yazidi men and took all their women and children as slaves.

If Shafii, Hanbalis or Salafists of today form an Islamic State/Caliphate today, then again they will start killing all the polytheists (including Atheists) and will not accept any Jizya from them. In this regard, there is no difference of opinion between ISIS and the Salafists (and all the followers of Imam Sahafii and Ahmed bin Hanbal). 

 


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