Muhammad says your "lives and property" are not safe from him unless you become a Muslim

In Sahih al-Bukhari and Sahih Muslim, the two most canonical hadith collections:

Bukhari, Volume 1, Book 2, Number 24:

Narrated Ibn 'Umar:

Allah's Apostle said: "I have been ordered (by Allah) to fight against the people until they testify that none has the right to be worshipped but Allah and that Muhammad is Allah's Apostle, and offer the prayers perfectly and give the obligatory charity, so if they perform all that, then they save their lives and property from me except for Islamic laws and then their reckoning (accounts) will be done by Allah."

Sahih Muslim, Book 031, Number 5917:

...Ali went a bit and then halted and did not look about and then said in a loud voice: Allah's Messenger, on what issue should I fight with the people? Thereupon he (the Prophet) said: Fight with them until they bear testimony to the fact that there is no god but Allah and Muhammad is his Messenger, and when they do that then their blood and their riches are inviolable from your hands but what is justified by law and their reckoning is with Allah.

Muhammad presides over the beheading of 600 to 900 Jews

From page 464 (690 in the Arabic) of the earliest Muslim biography of Muhammad:

Then [the Banu Qurayza tribe] surrendered, and the apostle [Muhammad] confined them in Medina in the quarter of d. al-Harith, a woman of B. al-Najjar. Then the apostle went out to the market of Medina (which is still its market today) and dug trenches in it. Then he sent for them and struck off their heads in those trenches as they were brought out to him in batches. Among them was the enemy of Allah Huyayy b. Akhtab and Ka`b b. Asad their chief. There were 600 or 700 in all, though some put the figure as high as 800 or 900. As they were being taken out in batches to the apostle they asked Ka`b what he thought would be done with them. He replied, 'Will you never understand? Don't you see that the summoner never stops and those who are taken away do not return? By Allah it is death!' This went on until the apostle made an end of them.

Muhammad says, "Fight everyone in the way of God and kill those who disbelieve in God."

Muhammad says those words on page 672 (992 in the Arabic) of the earliest Muslim biography of Muhammad.

Muhammad says, "kill any Jew who falls into your power."

He says it on page 369 (554 in the Arabic) of the earliest Muslim biography of Muhammad. It's a "beautiful" story of two brothers, Muhayyissa and Huwayyisa: (To avoid confusing the two brothers, keep in mind that the brother whose name begins with M is the Murderer in the story.)

"The apostle [Muhammad] said, ‘Kill any Jew that falls into your power.' Thereupon Muhayyisa bin Masud leapt upon Ibn Sunayna, a Jewish merchant with whom they had social and business relations, and killed him. Huwayyisa was not a Muslim at the time though he was the elder brother. When Muhayyisa killed [the Jewish merchant], Huwayyisa began to beat [his brother Muhayyisa], saying, 'You enemy of God, did you kill him when much of the fat on your belly comes from his wealth?' Muhayyisa answered, 'Had the one who ordered me to kill him ordered me to kill you I would have cut your head off.'...[Huwayyisa] replied, 'By God, if Muhammad had ordered you to kill me would you have killed me?' [Muhayyisa] said, 'Yes, by God, had he ordered me to cut off your head I would have done so.' [Huwayyisa] exclaimed, "By God, a religion which can bring you to this is marvellous!' and [Huwayyisa] became a Muslim."

To speed understanding of the above passage, I introduced into it specific names (in brackets), in place of some of the pronouns ("he," "him," etc.) that are in the original text.

Muhammad permits a threat of beheading to force a conversion to Islam

On page 547 (814 in the Arabic) of the earliest Muslim biography of Muhammad:

[Muhammad] said: "Woe to you Abu Sufyan, isn't it time that you recognize that I am God's apostle?" [Sufyan] answered, "As to that I still have some doubt." [Ibn Abbas] said to [Sufyan], "Submit and testify that there is no God but Allah and that Muhammad is the apostle of God before you lose your head," so [Sufyan] did so.

Canonical hadiths say Muhammad (in his fifties) consummated his marriage to Aisha when she was nine (lunar) years old

A lunar year is about 355 days long, which means that at consummation, Aisha may actually have been as young as 8 years and 9 months old (in 365-day years).

Some examples from al-Bukhari, the most canonical hadith collection:

Sahih al-Bukhari, Volume 7, Book 62, Number 64:

Narrated 'Aisha:

that the Prophet married her when she was six years old and he consummated his marriage when she was nine years old, and then she remained with him for nine years (i.e., till his death).
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Sahih al-Bukhari, Volume 7, Book 62, Number 65:

Narrated 'Aisha:

that the Prophet married her when she was six years old and he consummated his marriage when she was nine years old. Hisham said: I have been informed that 'Aisha remained with the Prophet for nine years (i.e. till his death)."
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Sahih al-Bukhari, Volume 7, Book 62, Number 88:

Narrated 'Ursa:

The Prophet wrote the (marriage contract) with 'Aisha while she was six years old and consummated his marriage with her while she was nine years old and she remained with him for nine years (i.e. till his death).
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Sahih al-Bukhari, Volume 5, Book 58, Number 236:

Narrated Hisham's father:

Khadija died three years before the Prophet departed to Medina. He stayed there for two years or so and then he married 'Aisha when she was a girl of six years of age, and he consumed that marriage when she was nine years old.

Had Aisha reached puberty at age 9 when Muhammad, in his fifties, consummated the marriage with her? No...

In another post, we cited some of the canonical hadiths in which it is stated that Muhammad consummated his marriage with Aisha when she was nine (lunar) years old. Had Aisha reached puberty by then?

Consider Sahih Muslim, a canonical hadith collection:

Book 008, Number 3311:

'A'isha (Allah be pleased with her) reported that Allah's Apostle (may peace be upon him) married her when she was seven years old, and she was taken to his house as a bride when she was nine, and her dolls were with her; and when he (the Holy Prophet) died she was eighteen years old.

In the next hadith, we learn that playing with dolls is only permitted for prepubescent children:

From Sahih al-Bukhari, a canonical hadith collection:

Volume 8, Book 73, Number 151:

Narrated 'Aisha:

I used to play with the dolls in the presence of the Prophet, and my girlfriends also used to play with me. When Allah's Apostle used to enter (my dwelling place) they used to hide themselves, but the Prophet would call them to join and play with me. (The playing with the dolls and similar images is forbidden, but it was allowed for 'Aisha at that time, as she was a little girl, not yet reached the age of puberty.) (Fateh-al-Bari page 143, Vol.13)

The parenthetical statement is not mine -- it's in the source Sahih al-Bukhari online, as you can see by clicking on the link above.  So, from the two canonical hadiths just cited, we find that 1) when Aisha, at the age of nine lunar years, entered Muhammad's house as a bride, her dolls were still with her, and 2) playing with dolls is permitted only to prepubescent children.

And then of course there is the increasingly infamous Qur'an verse 65:4, which specifies a waiting period for prepubescent females to remarry after being divorced. A waiting period before remarriage is required only if the dissolved marriage was consummated. (See Quran 33:49.) Thus Qur'an 65:4 assumes consummation with prepubescent girls.

Qur'an Chapter 65, Verse 4:

And (as for) those of your women who have despaired of menstruation [because post-menopausal], if you have a doubt, their prescribed [waiting] time shall be three months, and of those too who have not had their courses [because prepubescent]; and (as for) the pregnant women, their prescribed time is that they lay down their burden; and whoever is careful of (his duty to) Allah He will make easy for him his affair.

In yet another post on this question, I'll quote a number of authoritative, mainstream Muslim scholars who agree that 65:4 refers to the waiting period before remarriage of divorced, prepubescent girls.

Top Islamic scholars' explanations of Qur'an 65:4 show that the verse assumes consummation of marriage with prepubescent girls

Before quoting the scholars on Quran 65:4, it should be noted that Quran 33:49 lays down that when a divorced female is to marry a new spouse, a waiting period is required only if the previous marriage was consummated. The scholars I will be quoting below all know this.  One of them, Maududi, mentions and explains it.

With that in mind, first consider Ibn Abbas, a companion of Muhammad, and one of many authorities who affirm that Qur'an 65:4 refers to the waiting period for prepubescent girls to remarry after divorce.

Ibn Abbas paraphrasing and explaining Quran 65:4

(And for such of your women as despair of menstruation) because of old age, (if ye doubt) about their waiting period, (their period (of waiting) shall be three months) upon which another man asked: “O Messenger of Allah! What about the waiting period of those who do not have menstruation because they are too young?” (along with those who have it not) because of young age, their waiting period is three months. Another man asked: “what is the waiting period for those women who are pregnant?” (And for those with child) i.e. those who are pregnant, (their period) their waiting period (shall be till they bring forth their burden) their child. (And whosoever keepeth his duty to Allah) and whoever fears Allah regarding what he commands him, (He maketh his course easy for him) He makes his matter easy; and it is also said this means: He will help him to worship Him well.

Some eight hundred years later appeared the Tafsir al-Jalalayn, one of the most widely used interpretations of the Qur'an. Tafsir al-Jalalayn also paraphrases Quran 65:4 and says part of it speaks of the waiting period before remarriage of divorced, prepubescent girls:

And [as for] those of your women who (read allā’ī or allā’i in both instances) no longer expect to menstruate, if you have any doubts, about their waiting period, their prescribed [waiting] period shall be three months, and [also for] those who have not yet menstruated, because of their young age, their period shall [also] be three months — both cases apply to other than those whose spouses have died; for these [latter] their period is prescribed in the verse: they shall wait by themselves for four months and ten [days] [Q. 2:234]. And those who are pregnant, their term, the conclusion of their prescribed [waiting] period if divorced or if their spouses be dead, shall be when they deliver. And whoever fears God, He will make matters ease for him, in this world and in the Hereafter.

65:4, according to Wahidi's respected explanation of the Quran:

(And for such of your women as despair of menstruation…) [65:4]. Said Muqatil: “When the verse (Women who are divorced shall wait, keeping themselves apart…), Kallad ibn al-Nu‘man ibn Qays al-Ansari said: ‘O Messenger of Allah, what is the waiting period of the woman who does not menstruate and the woman who has not menstruated yet? And what is the waiting period of the pregnant woman?’ And so Allah, exalted is He, revealed this verse”. Abu Ishaq al-Muqri’ informed us Muhammad ibn ‘Abd Allah ibn Hamdun Makki ibn ‘Abdan Abu’l-Azhar Asbat ibn Muhammad Mutarrif Abu ‘Uthman ‘Amr ibn Salim who said: “When the waiting period for divorced and widowed women was mentioned in Surah al-Baqarah, Ubayy ibn Ka‘b said: ‘O Messenger of Allah, some women of Medina are saying: there are other women who have not been mentioned!’ He asked him: ‘And who are they?’ He said: ‘Those who are too young [such that they have not started menstruating yet], those who are too old [whose menstruation has stopped] and those who are pregnant’. And so this verse (And for such of your women as despair of menstruation…) was revealed”.

The bracketed text is not me, it's in the Wahidi at Altafsir.com.

Ibn Kathir is perhaps the Muslim world's most respected Quran expositor.

Kathir says of 65:4 

Allah the Exalted clarifies the waiting period of the woman in menopause. And that is the one whose menstruation has stopped due to her older age. Her `Iddah [waiting period before remarriage] is three months instead of the three monthly cycles for those who menstruate, which is based upon the Ayah [verse] in (Surat) Al-Baqarah. (see Qur'an 2:228) The same for the young, who have not reached the years of menstruation. Their `Iddah [waiting period before remarriage] is three months like those in menopause. This is the meaning of His [Allah's] saying;

 [Qur'an 65:4] (and for those who have no courses...)

Syed Abul Ala Maududi (died 1979), another famous Qur'an expositor, says of Quran 65:4:

Here, one should bear in mind the fact that according to the explanations given in the Quran the question of the waiting period arises in respect of the women with whom marriage may have been consummated, for there is no waiting-period in case divorce is pronounced before the consummation of marriage. (Al-Ahzab: 49) [Quran Chapter 33, Verse 49]. Therefore, [the Quran] making mention of the waiting-period for the girls who have not yet menstruated, clearly proves that it is not only permissible to give away the girl in marriage at this age but it is also permissible for the husband to consummate marriage with her. Now, obviously no Muslim has the right to forbid a thing which the Quran has held as permissible.

So major Muslim expositors of the Quran agree that Quran 65:4 assumes and supports consummation of marriage with prepubescent girls. These expositors know what Maududi above mentions: per Quran 33:49, a waiting period before remarriage is only required if the dissolved marriage was consummated.

Also, many Muslim translations of 65:4 make absolutely clear that the verse refers to the waiting period before remarriage of prepubescent girls. See for example these translations: Al-Muntakahb, Abdel Haleem, Abdul Majid Daryabadi, Aisha Bewley, Ali Quli Qara'i, Muhammad Mahmoud Ghali, Muhammad Taqi Usmani.

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Also, from Sahih al-Bukhari, the most canonical hadith collection, see this hadith which refers to the waiting period for girls "before puberty":

Volume 7, Book 62, Number 63:

Narrated Sahl bin Sad:

While we were sitting in the company of the Prophet a woman came to him and presented herself (for marriage) to him. The Prophet looked at her, lowering his eyes and raising them, but did not give a reply. One of his companions said, "Marry her to me O Allah's Apostle!" The Prophet asked (him), "Have you got anything?" He said, "I have got nothing." The Prophet said, "Not even an iron ring?" He Sad, "Not even an iron ring, but I will tear my garment into two halves and give her one half and keep the other half." The Prophet; said, "No. Do you know some of the Quran (by heart)?" He said, "Yes." The Prophet said, "Go, I have agreed to marry her to you with what you know of the Qur'an (as her Mahr)." 'And for those who have no courses (i.e. they are still immature). (Qur'an 65.4) And the 'Iddat [waiting period before remarriage] for the girl before puberty is three months (in the above Verse).

[The last lines are what the man knows of the Quran.]

Muhammad speaks of help from terror, his right to spoils of war, and his mission to all mankind

In a canonical hadith collection, Sahih Muslim:

Book 4, Number 1062:

Abu Huraira reported that the Messenger of Allah [Muhammad] (may peace be upon him) said: I have been given superiority over the other prophets in six respects: I have been given words which are concise but comprehensive in meaning; I have been helped by terror (in the hearts of enemies): spoils have been made lawful to me: the earth has been made for me clean and a place of worship; I have been sent to all mankind and the line of prophets is closed with me.

Notice that by declaring in the above hadith that he is the final prophet, Muhammad tried to cut off the possibility of anyone claiming equal status with him; another prophet might effectively challenge Muhammad's authenticity. More significant, Muhammad, in speaking of help from terror, displays again to those who know the core Islamic texts just how far he was willing to go to dominate competing forms of "prophecy," expression, and worldview.

Muhammad says the minds of women are deficient

In Sahih al-Bukhari, the most canonical hadith collection:

Volume 3, Book 48, Number 826:

Narrated Abu Said Al-Khudri:

The Prophet said, "Isn't the witness of a woman equal to half of that of a man?" The women said, "Yes." He said, "This is because of the deficiency of a woman's mind."

Muhammad says a woman should not travel without a male custodian

In Sahih al-Bukhari, the most canonical hadith collection:

Volume 4, Book 52, Number 250:

Narrated Ibn Abbas:

That he heard the Prophet saying, "It is not permissible for a man to be alone with a woman, and no lady should travel except with a Muhram [legal custodian] (i.e. her husband or a person whom she cannot marry in any case for ever; e.g. her father, brother, etc.)." Then a man got up and said, "O Allah's Apostle! I have enlisted in the army for such-and-such Ghazwa [raid or battle] and my wife is proceeding for Hajj [pilgrimage]." Allah's Apostle said, "Go, and perform the Hajj with your wife."

The Qur'an does not say beat your wife if she is disobedient; it says beat her if you merely "fear" or suspect disobedience

Below are ten translations of a notorious portion of Qur'an 4:34, the beat-your-disobedient-wife verse. 

Six of the ten translations use the word "beat."

Two translations use the word "scourge," which as a verb means to whip.

And two of the translations use the word "chastise." Most dictionaries give corporal punishment (beating, or "stripes") as one of the main definitions of "chastise."

Some of the translators insert softening words in parentheses. None of the insertions in parentheses are in the original Arabic of the Qur'an.

Pickthall: "and scourge them"
Yusuf Ali: "(And last) beat them (lightly)"
Al-Hilali/Khan: "(and last) beat them (lightly, if it is useful)"
Shakir: "and beat them"
Sher Ali: "and chastise them"
Khalifa: "then you may (as a last alternative) beat them"
Arberry: "and beat them"
Rodwell: "and scourge them"
Sale: "and chastise them"
Asad: "then beat them"
Dawood: "and beat them."

Here's Aisha Bewley's version of Quran 4:34:

Men have charge of women because Allah has preferred the one above the other and because they spend their wealth on them. Right-acting women are obedient, safeguarding their husbands’ interests in their absence as Allah has guarded them. If there are women whose disobedience you fear, you may admonish them, refuse to sleep with them, and then beat them. But if they obey you, do not look for a way to punish them. Allah is All-High, Most Great.

Examples of Islam's founders striking women

From Sahih al-Bukhari and Sahih Muslim, the two most canonical hadith collections:

Sahih al-Bukhari, Volume 8, Book 82, Number 828:

Narrated Aisha [Muhammad's favorite wife]:

Abu Bakr [first caliph, father of Aisha, and companion of Muhammad] came towards me and struck me violently with his fist and said, "You have detained the people because of your necklace." But I remained motionless as if I was dead lest I should awake Allah's Apostle although that hit was very painful.

Sahih Muslim, Book 009, Number 3506:

Jabir b. 'Abdullah (Allah be pleased with them) reported: Abu Bakr...came and sought permission to see Allah's Messenger...He found people sitting at his door and none amongst them had been granted permission, but it was granted to Abu Bakr and he went in. Then came Umar and he sought permission and it was granted to him, and he found Allah's Apostle...sitting sad and silent with his wives around him. He (Hadrat Umar) said: I would say something which would make the Holy Prophet...laugh, so he [Umar] said: Messenger of Allah, I wish you had seen (the treatment meted out to) the daughter of Khadija when you asked me some money, and I got up and slapped her on her neck. Allah's Messenger [Muhammad]...laughed and said: They are around me as you see, asking for extra money. Abu Bakr [who was later to become first caliph]...then got up went to A'isha...and slapped her on the neck, and Umar [who was later to become second caliph] stood up before Hafsa and slapped her saying: You ask Allah's Messenger...which he does not possess. They said: By Allah, we do not ask Allah's Messenger...for anything he does not possess...

Sahih Muslim, Book 004, Number 2127:

...(the Holy Prophet) entered the (house), and said: Why is it, O 'A'isha, that you are out of breath? I said: There is nothing. He said: Tell me or the Subtle and the Aware would inform me. I said: Messenger of Allah, may my father and mother be ransom for you, and then I told him (the whole story). He said: Was it the darkness (of your shadow) that I saw in front of me? I said: Yes. He [Muhammad] struck me on the chest which caused me pain, and then said: Did you think that Allah and His Apostle would deal unjustly with you?...

Sahih al-Bukhari Volume 7, Book 72, Number 715:

Narrated 'Ikrima:

Rifa'a divorced his wife whereupon 'AbdurRahman bin Az-Zubair Al-Qurazi married her. 'Aisha said that the lady (came), wearing a green veil (and complained to her (Aisha) of her husband and showed her a green spot on her skin caused by beating). It was the habit of ladies to support each other, so when Allah's Apostle came, 'Aisha said, "I have not seen any woman suffering as much as the believing women. Look! Her skin is greener than her clothes!"...

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Wife-beating goes on in all societies. Most societies seek to punish it. Islam's core texts and founders, with some limitations, make it into something ordered by God (see the post on Quran 4:34) and thus very difficult to reform.

Muhammad says that one day the very trees and stones will help Muslims to kill Jews

He says it in both Sahih al-Bukhari and Sahih Muslim, Islam's two most canonical hadith collections:

Sahih al-Bukhari, Volume 4, Book 56, Number 791:

Narrated 'Abdullah bin 'Umar:
I heard Allah's Apostle [Muhammad] saying, "The Jews will fight with you, and you will be given victory over them so that a stone will say, 'O Muslim! There is a Jew behind me; kill him!' "

Sahih al-Bukhari, Volume 4, Book 52, Number 176:

Narrated 'Abdullah bin 'Umar:
Allah's Apostle said, "You (i.e. Muslims) will fight with the Jews till some of them will hide behind stones. The stones will (betray them) saying, 'O 'Abdullah (i.e. slave of Allah)! There is a Jew hiding behind me; so kill him.' "

Sahih al-Bukhari, Volume 4, Book 52, Number 177:

Narrated Abu Huraira:
Allah's Apostle said, "The Hour will not be established until you fight with the Jews, and the stone behind which a Jew will be hiding will say. "O Muslim! There is a Jew hiding behind me, so kill him."

Sahih Muslim, Book 041, Number 6981:

Ibn 'Umar reported Allah's Messenger [Muhammad] (may peace be upon him) as saying: You will fight against the Jews and you will kill them until even a stone would say: Come here, Muslim, there is a Jew (hiding himself behind me); kill him.

Sahih Muslim, Book 041, Number 6983:

Abdullah b. 'Umar reported Allah's Messenger (may peace be upon him) as saying: You and the Jews would fight against one another until a stone would say: Muslim, here is a Jew behind me; come and kill him.

Sahih Muslim, Book 041, Number 6984:

Abdullah b. 'Umar reported that Allah's Messenger (may peace be upon him) said: The Jews will fight against you and you will gain victory over them until the stone would say: Muslim, here is a Jew behind me; kill him.

Sahih Muslim Book 041, Number 6985:

Abu Huraira reported Allah's Messenger (may peace be upon him) as saying: The last hour would not come unless the Muslims will fight against the Jews and the Muslims would kill them until the Jews would hide themselves behind a stone or a tree and a stone or a tree would say: Muslim, or the servant of Allah, there is a Jew behind me; come and kill him; but the tree Gharqad would not say, for it is the tree of the Jews.

Muhammad says Muslims in a position of strength should impose three choices on non-Muslims: 1) become Muslim; or 2) pay protection money for the right to live precariously, as a second-class citizen; or 3) be killed

In Sahih Muslim, a canonical hadith collection:

Book 019, Number 4294

...the Messenger of Allah [Muhammad] (may peace be upon him)...would say: Fight in the name of Allah and in the way of Allah. Fight against those who disbelieve in Allah. Make a holy war...When you meet your enemies who are polytheists ["polytheists" to Islamic scholars broadly includes Christians and Jews, because of, for example, Quran 9:30 and 9:31] invite them to three courses of action. If they respond to any one of these, you also accept it and withhold yourself from doing them any harm. [1] Invite them to (accept) Islam; if they respond to you, accept it from them and desist from fighting against them. ...[2] If they refuse to accept Islam, demand from them the Jizya [protection money non-Muslims must pay to Muslim overlords for the right to live, and as an indication of Muslim superiority and non-Muslims' "state of subjection" spoken of in Qur'an 9:29. For proof, see also this]. If they agree to pay, accept it from them and hold off your hands. [3] If they refuse to pay the tax, seek Allah's help and fight them...

Muhammad orders people burned up in their houses, for not coming to prayer

In Sahih al-Bukhari, the most canonical hadith collection:
Volume 1, Book 11, Number 626:

Narrated Abu Huraira:

The Prophet said, "No prayer is harder for the hypocrites than the Fajr [pre-dawn] and the 'Isha' [evening] prayers and if they knew the reward for these prayers at their respective times, they would certainly present themselves (in the mosques) even if they had to crawl." The Prophet added, "Certainly I decided to order the Mu'adh-dhin (call-maker) to pronounce Iqama [second call to prayer] and order a man to lead the prayer and then take a fire flame to burn all those who had not left their houses so far for the prayer along with their houses."

Volume 1, Book 11, Number 617:

Narrated Abu Huraira:

Allah’s Apostle said,“By Him in Whose Hand my soul is I was about to order for collecting fire-wood (fuel) and then order someone to pronounce the Adhan [summons] for the prayer and then order someone to lead the prayer then I would go from behind and burn the houses of men who did not present themselves for the (compulsory congregational) prayer. By Him, in Whose Hands my soul is, if anyone of them had known that he would get a bone covered with good meat or two (small) pieces of meat present in between two ribs, he would have turned up for the ‘Isha’ prayer.’[fifth of the five daily prayers]

Muhammad rejects religious pluralism

For example, in Sahih Muslim, a canonical hadith collection:

Book 19.4366

It has been narrated by 'Umar b. al-Khattib that he heard the Messenger of Allah [Muhammad] (may peace be upon him) say:"I will expel the Jews and Christians from the Arabian Peninsula and will not leave any but Muslim."

The Qur'an says non-Muslims will be punished with hooked rods of iron

Quran 22:19 to 22:22:

These twain (the believers and the disbelievers) are two opponents who contend concerning their Lord. But as for those who disbelieve, garments of fire will be cut out for them; boiling fluid will be poured down on their heads,

Whereby that which is in their bellies, and their skins too, will be melted;

And for them are hooked rods of iron.

Whenever, in their anguish, they would go forth from thence they are driven back therein and (it is said unto them): Taste the doom of burning.

Ibn Kathir, likely the Muslim world's most respected Quran commentator, says Allah's pardon of the unbelievers was canceled by Quran Chapter 9 and its verses of the sword

Kathir explains here (if you go there, scroll down to the bottom third of the page) that Quran 2:109, which he quotes without giving its chapter and verse number, and which advises Muslims to be tolerant toward unbelievers, has been canceled by verses in Quran Chapter 9 (which Muslim scholars generally agree was one of the last Quran chapters revealed). Kathir quotes part of Quran 9:5, but here's the whole verse:

Then, when the sacred months have passed, slay the idolaters wherever ye find them, and take them (captive), and besiege them, and prepare for them each ambush. But if they repent and establish worship and pay the poor-due, then leave their way free. Lo! Allah is Forgiving, Merciful.

And Kathir quotes part of Quran 9:29. Again, here's the whole verse:

Fight those who do not believe in Allah, nor in the latter day, nor do they prohibit what Allah and His Messenger [Muhammad] have prohibited, nor follow the religion of truth [Islam], out of those who have been given the Book [the Bible, given to Christian and Jews], until they pay the tax in acknowledgment of [Muslim] superiority and they are in a state of subjection [this subjection is a source of Islamic law's institution of dhimmitude, i.e., third-class legal status for non-Muslims].

Notice that 9:29 does not say "fight in self-defense." It says "fight those who do not believe" in Islam.

Anyway, then Kathir says,

Allah's pardon for the disbelievers was repealed. Abu Al-`Aliyah, Ar-Rabi` bin Anas, Qatadah and As-Suddi said similarly: "It [the pardon, or forgiveness] was abrogated by the Ayah [verse] of the sword." [The verse of the sword is Qur'an 9:5 ]

"I will cast terror into the hearts of those who disbelieve. Therefore strike off their heads..."

That headline is from Qur'an Chapter 8, Verse 12:

When your Lord revealed to the angels: I am with you, therefore make firm those who believe. I will cast terror into the hearts of those who disbelieve. Therefore strike off their heads and strike off every fingertip of them.