I want to first establish that the vast majority of Muslims are peaceful people. They are not intrinsically violent people as some would have us believe. Yet, when the Qur'an and Hadith are examined with context in mind, it is evident that the very literature that Islam promotes violence.
Muslims, in an attempt to defend Islam, will often point to other verses in the Qur'an and Hadith which seemingly promote peace. Furthermore, they will often manufacture false contexts for passages to make it seem as if though violence was not being promoted offensively, but rather defensively.
In response to this, it needs to be made clear that the Qur'an is not chronologically ordered. When the Qur'an's passages are chronologically ordered, a shift from peace in earlier passages towards violence in later passages becomes clear. The Islamic teaching of 'naskh' or 'abrogation' means that later revelations abrogate or supersede earlier revelations when they are in tension. Qur'an 2:106, 13:39, and 16:101 are relevant passages on this Islamic teaching.
We do not abrogate a verse or cause it to be forgotten except that We bring forth [one] better than it or similar to it. Do you not know that Allah is over all things competent? (Qur'an 2:106, Sahih International)
Allah eliminates what He wills or confirms, and with Him is the Mother of the Book. (Qur'an 13:39, Sahih International)
And when We substitute a verse in place of a verse - and Allah is most knowing of what He sends down - they say, "You, [O Muhammad], are but an inventor [of lies]." But most of them do not know. (Qur'an 16:101, Sahih International)
Going back to the context of Qur'an 2:106, we see something interesting in ayah 109. It talks about how the 'People of the Scripture' (Jews and Christians) which were trying to dissuade Muslims from believing in Islam. Muslims were told to 'pardon and overlook' the actions of these Jews and Christians 'until Allah delivers His command.' When Allah gives that new command, Muslims would no longer need to pardon and overlook these actions.
Many of the People of the Scripture wish they could turn you back to disbelief after you have believed, out of envy from themselves [even] after the truth has become clear to them. So pardon and overlook until Allah delivers His command. Indeed, Allah is over all things competent. (Qur'an 2:109, Sahih International)
In fact, this occurred once Qur'an 9:29 was revealed. At that point, Muslims were explicitly commanded to fight those (1) who do not believe in Allah or the last day, (2) who do not consider unlawful what Allah and His Messenger have made unlawful, and (3) who do not adopt the religion of truth from those who were given the Scripture. Woah, that abrogates the pardoning and overlooking of Qur'an 2:109. Unless they paid jizyah, they were to be killed
Fight those who do not believe in Allah or in the Last Day and who do not consider unlawful what Allah and His Messenger have made unlawful and who do not adopt the religion of truth from those who were given the Scripture - [fight] until they give the jizyah willingly while they are humbled. (Qur'an 9:29, Sahih International)
In Qur'an 9:5, we see the similar fate of the polytheists. Unless they repented, established prayer, and paid zakah, they were to be killed wherever they where found.
And when the sacred months have passed, then kill the polytheists wherever you find them and capture them and besiege them and sit in wait for them at every place of ambush. But if they should repent, establish prayer, and give zakah, let them [go] on their way. Indeed, Allah is Forgiving and Merciful. (Qur'an 9:5, Sahih International)
I bring up surah 9, known as Surah At-Tawbat or Surah Al-Bara'ah, because it is clear from Hadith (Sahih al-Bukhari, Vol. 6, Book 60, No. 129) that it is the last surah chronologically. Therefore, surah 9 contains the final marching orders of Allah and Muhammad.
The last Sura that was revealed was Bara'a, and the last Verse that was revealed was: "They ask you for a legal verdict, Say: Allah's directs (thus) about those who leave no descendants or ascendants as heirs." (4.176) (Sahih al-Bukhari: Vol. 6, Book 60, No. 129)
Peace is not what is being promoted here. Offensive violence is what is being promoted here. As per the Islamic teaching of abrogation, a verse can only be superseded by something better. It is clear therefore that Allah and Muhammad view violence as something better than peace.
Though the Islamic conception of Allah would rather punish than pardon and overlook, the Judeo-Christian God is one who pardons all iniquities and covers them. Infinite justice could only be satisfied when the infinite God took it upon Himself on the Cross of Calvary. This God with such as self-sacrificial love does not want any to perish but for all to come to repentance.
“And their sins and their lawless deeds
I will remember no more.” (Hebrews 10:17, NASB)
The Lord is not slow about His promise, as some count slowness, but is patient toward you, not wishing for any to perish but for all to come to repentance. (2 Peter 3:9, NASB)
The judgements which the Judeo-Christian God carried out against nations in the Old Testament were warranted, were the result of much patience, and were specific in scope. The wars were against nations that had committed heinous iniquities such as passing children through the fire in sacrifice to gods such as Molech (Leviticus 18:21, Leviticus 18:24-30, Deuteronomy 18:9-11). We see God's patience with how He waited 4 generations or 400 years before carrying out judgement against the Amorites (Genesis 15:13,16). He eventually gave a specific command to the Israelites concerning such nations with further guidance along the way (Deuteronomy 20:17).
Ultimately, we have to understand these judgements, and the judgments in the Mosaic law given specifically for Old Testament Israelites, were commanded by the one who is the objective point of reference for morality. In situations where an individual disagrees with God's judgements, it is important to remember it is futile to think that one's subjective perception of morality supersedes an objective point of reference for morality. In the case of Islam, unlike the Judeo-Christian worldview, the judgements proceed from what is clearly a false religion.
What is in found in the Judeo-Christian texts are in stark contrast to the offensive wars waged by Muhammad against polytheists and Jews and Christians. Various Islamic texts, including the open-ended last marching order found in surah 9, are a legitimate basis for the deadly consequences of Islamism in our world.
Notes made on David Wood's video on the three stages of jihad:
1. STEALTH JIHAD
When Muhammad and his followers were a persecuted minority in Mecca, they criticized the beliefs of the polytheists but did so peacefully. During this time, Muhammad outwardly pointed to a final judgement. Qur'an 109 talks about religions coexisting.
Yet, according to At-Tabari, Volume VI, p.95, Muhammad was already plotting how he could get non-Arabs to submit by making them say there is no deity but Allah. They're not attacking him, but he already has plans.
Qur'an 3:28 talks about how Muslims should not be friends with unbelievers except they need them as security. Essentially as coverage because Muslims are in the minority. Ibn Kathir says "In this case, Muslims are allowed to show friendship outwardly but never inwardly." Abu Darda says "We smile in the face of some people even though our hearts curse them."
At-Tabari, Volume VI, p. 93 talks about how Muslims were not rejected by the Pagans in Mecca until Muslims started denouncing their gods. On p. 101 it is clear that their denouncing was not as innocent as it sounds. Muslims wanted victim-status.
When Muslims were being persecuted, Christians, Jews, Syrians and more came to their aid to protect them from those in Mecca. Yet, little did they know that Muhammad had plotted against them.
Once Muhammad had developed enough alliances, the message of the Qur'an suddenly changed.
2. DEFENSIVE JIHAD
Fighting unbelievers who pose a physical or intellectual threat to Islam. Qur'an 22:39-40 talks about permission being given to 'defend' in war because they are 'oppressed.'
The people of Mecca depended on the caravan trade. Muhammad launched an attack on the Meccan caravans. 7 attacks were launched with no retaliation from Meccans. During the seventh attack, which happened during a holy month (where there was an agreement not to fight), one died and others were taken captive. This is when Muhammad had Qur'an 2:217 which talks about how persecution was worse than killing. Muhammad justified the killing.
At the next caravan was when Muslims had their first battle with non-Muslims. What was it really about? Non-Muslims defending themselves against Muslims.
The people who had earlier come to the defence of Muhammad and Muslims had found themselves trapped. They were subject to enslavement, punishment, and annihilation if they left Muhammad's unjust battles. Three Jewish tribes found this out the hard way. People who spoke out or wrote poems about Muhammad were brutally murdered.
3. OFFENSIVE JIHAD
When Muslims establish a majority in an area, they are commanded to begin offensive jihad. Once Mecca was under Muhammad's control, Muslims were to indiscriminately fight non-Muslims simply for being non-Muslims. Qur'an 9:73 talks about striving hard against the unbelievers in an unyielding way. Qur'an 9:111 talks about how Allah has bought persons as believers or his property so they can slay and be slain. Qur'an 9:123 mentions fighting again.
And I'll even go the often cited Qur'an 9:29 where Muslims are commanded to fight those who don't believe in Allah or the last day, or believe in something forbidden by Allah, or are Christian (people of the book) and don't acknowledge the 'religion of truth.' This is unless of course they pay a jizyah with willing submission. This isn't about oppressors or even critics, this is indiscriminate.
In trusted Hadith, Sahih al-Bukhari 6924, the same sentiment is clear. Furthermore, in Sahih Muslim 30, Muhammad is said to have said that he has been commanded to fight till they declare there is no God but Allah.
The same Muhammad who earlier said people were persecuting him based on what he believed was now persecuting others solely based on what they believed.
In Sahih Muslim 4366, Muhammad says he will expel the Jews and the Christians from the Arabian Peninsula and will not leave any but Muslims. Scary. Is this a man who promoted religious diversity and tolerance? Only when he was in the minority. Then diversity and tolerance went out the window along with Jews and Christians.