Let's begin by understanding islam's sacred texts. The first text and the most important is the Qur'an.
THE QUR'AN
It is the most important because unlike the gospels or the Bible, the Qur'an was not written by a man. For islam the Qur'an was written by God himself. It was only transmitted to Muhammad by the Angel Gabriel throughout all of his life, who then dictated it to his followers who wrote the revelations down. It is an important difference because it means that the Qur'an cannot be questioned without questioning God in the process.
Since the Qur'an was written by God himself, it's content is sacred, it cannot be questioned, it is immutable and permanent and it must be accepted in it's totality by any muslim man.
When it comes to the shape and content of the Qur'an it's extension is similar to the New Testament. It is divided into 114 Suras (something similar to a chapter) and each Sura contains several Ayahs which are verses.
If you read the Qur'an all the way through you will not understand it because the ahyas are not placed in chronological order. It isn't ordered thematically either. It is compiled by the length of the Suras: the longest Suras go first.
Another thing that makes the Qur'an hard to understand for someone who is reading it for the first time is the fact that many of it's ayahs are about events in the life of Muhammad that are not directly narrated on the Qur'an. In order to understand what those parts are about you need to first know what events they refer to and in order to know that you must be familiar with the life of Muhammad. A muslim who knows the life of Muhammad in detail and a westerner who doesn't will understand two different things when they read the Qur'an.
The islamic theology divides the Suras in 2 categories: the suras that were revealed in Mecca, and the suras that were revealed in Medina. They are divided in such way because Muhammad's life had two parts: at the beginning, Muhammad lived with his followers in Mecca and they were a vulnerable minority under the rule of the polytheists. Then he had to flee Mecca to Medina and while in Medina Muhammad became the leader of an army that conquered the entire area.
While in Mecca Muhammad revealed many pacific ideas, for example, the idea that religion should be free and you cannot force another person to adopt islam.
This pacific fragment was revealed in Meca:
Say “Oh disbelievers,
I do not worship what you worship.
Nor are you worshippers of what I worship.
Nor will I be a worshipper of what you worship.
For you is your religion and for me is my religion.”
(109)
And this other pacific fragment was revealed soon after, when they had just fled Mecca and were settling in Medina:
There shall be no compulsion in [acceptance of] the religion. The right course has become clear from the wrong. So whoever disbelieves in Taghut and believes in Allah has grasped the most trustworthy handhold with no break in it. And Allah is Hearing and Knowing.
(2:256)
But after settling in Medina, Muhammad became a truly powerful leader. He started to amass a great following, took over the city, and then started to wage a war of conquest against all its neighbors. As Muhammad became more powerful the tone of his revelations changed from peaceful to violent.
In Medina, Muhammad revealed that the infidels must be captured, sieged, and killed unless they converted and did the muslim prayers, and paid the muslim tax. He revealed that incredulity must be erradicated until the only religion left in the world was islam. He revealed Allah has enemies that must be defeated by force and you must massacre the enemies of Allah if you want access to the afterlife.
These are some of the violent fragments that were revealed in Medina:
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.
(9:5)
And fight them until there is no incredulity and until the religion, all of it, is for Allah. And if they cease - then indeed, Allah is Seeing of what they do.
(8:39)
It is proper for a prophet to keep captives of war until he inflicts a massacre upon Allah 's enemies in the land. Some Muslims desire the commodities of this world, but Allah desires for you the Hereafter. And Allah is Exalted in Might and Wise.
(8:67)
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 them until they give the jizyah willingly while they are humbled.
(9:29)
In short: the Qur'an orders explicitly to not impose religion by force while at the same time orders to fight against anyone who is not a muslim until they die or convert. The Qur'an teaches to respect the monotheists (those who were given the Scripture), but then it orders to to subjugate them. It teaches to tolerate the pagan and at the same time it teaches that a great massacre must be inflicted upon them.
The muslim believer then seems to be facing a contradiction that it is impossible to resolve: it is impossible to accept all of the Qur'an and apply it when two of it's parts contradict each other. In order to follow one of the parts you must disobey the other.
But if the Qur'an was written by God and it is eternal, how can it admit contradictions? Can God change his mind? If the answer is "yes" then, how do we know which one of his opinions we should follow and which one to discard? How can a muslim accept one part of the qur'an and reject another?
Facing all these contradictions in his revelations and trying to give an answer to his followers' questions, Muhammad revealed the principle of abrogation which is a part of the Qur'an and basically states that if two verses in the Qur'an contradict each other then the most recent one is the one you should follow as it supersedes the older one and "annuls" it:
We do not abrogate a verse or cause it to be forgotten except when We bring forth [one] better than it or similar to it. Do you not know that Allah is over all things competent?
(2:106)
What this ayah indicates is that the most recent verses annul the older verses. Meaning that if you find 2 verses that contradict each other you need to find out which one was revealed first and which one was revealed later because the second one annuls the first.
Following the principle of abrogation we realize that the violent passages that were revealed in Medina annul the peaceful ones that were revealed in Mecca. Meaning: between not imposing religion by force or fighting infidels until they convert, you must do the latter.
There are many contradictory ayah within the Qur'an, it isn't only about the fight against infidels. For example, when it comes to alcohol. In Mecca Muhammad revealed that alcohol and gambling were a sin but they also had benefits and the only thing that was forbidden was to drink during prayer (2:219), but later, in Medina, the ayah regarding alcohol became stricter until Muhammad forbid drinking and gambling altogether (5:91). Today, no muslim that follows their faith considers that drinking alcohol is allowed, as the second ayah annulled the first one.
Many things were imposed by Muhammad in Medina, like the penalty of death for apostates of the religion, he increased the severity of the punishments for transgressions, for theft, for fornication, and the permitted aggressions against women. The lax and pacific ayahs were all revealed in Meca and the violent and oppressive ayahs were revealed in Medina and since those were revealed later, they abrogate the first ones.
The vast majority of muslim authorities accept the principle of abrogation as valid but they differ in how it should be applied: which ayahs abrogate others. Most consider that an ayah that is revealed later will annul any similar ayah that was revealed before it. Some think only the ayahs that contradict each other must be annulled. A minority considers that the abrogation principle is valid but ayahs can only be abrogated or sustained depending on the context. What this means is that a muslim should act according to the pacific ayahs when his circumstances are similar to those Muhammad faced in Mecca: when he is living in a society of infidels in which muslims are a minority; and that he must act like Muhammad in Medina and follow the violent ayahs when he is in a country with a muslim majority or when there is an organized islamic army like the one Muhammad had in Medina.
The case is that big chunks of the Qur'an are not about spirituality, but about the war that must be waged against the infidels, the pagans, and the unbelievers with the purpose of expanding the umma which is the "muslim world". The Qur'an establishes the ways in which these objectives must be reached through physical violence as well as other types of subjugation. The Qur'an therefore is not only a religious text, but also the text of a political ideology.
They say that when the Qur'an is recited in arab by an expert it is a beautiful song because the Qur'an is originally written in verse and no translation can properly translate the poetic sense of it. The Qur'an as a written work of literature and as a melody can be an esthetically beautiful work, but ironically this quality only makes the message of intolerance that is written all across the text that more terrible. The problem of intolerance within the Qur'an is more than just a pair of isolated ayahs that were taken out of context, because it is one of the most important themes within the Qur'an. There are over 130 violent orders explicitly written in the Qur'an that must be performed by faithful muslims against anyone who is not a muslim.
In order to understand which ayahs abrogate others it is necessary to know which one was revealed first, but since the Qur'an is not written in chronological order muslims need to use a guide to understand at which point in his life Muhammad revealed each ayah and then reach a conclusion about which one of the two is valid. This guide is the Sunnah, which is the second sacred text in islam.
THE SUNNAH
The Qur'an says that morality flows out of the life of Muhammad and that every muslim must live their life according to the life of Muhammad. This means that the life of Muhammad is not measured against any external morality standards, but it is in itself the moral standard against which the lives of every muslim should be measured. (3:32, 3:164, 33:21) Therefore the way to serve Allah is emulating the actions that Muhammad took in life.
The life of Muhammad is compiled in the Sunnah which is divided into 2 bodies of text. On the one hand we have the hadiths which are the testimonies of his closest followers, something similar to the gospels. On the other hand is the sirah which is Muhammad's biography narrated in chronological order.
When it comes to the hadiths, there were thousands of testimonies, some were very long and took several pages, others were so short they took only a couple of lines. When they tried to put them into order, islam scholars discovered that there was a good chance that the majority of those hadiths were fake. Identifying the fake hadiths and separating them from the authentic ones was quite a task. Some branches of islam accept a few testimonies as valid, other branches accept others, but there are 2 that are universally accepted as authentic and those are the hadiths of Bukhari and Muslim. They contain 7000 and 12000 testimonies each, although some testimonies are in there more than once.
What is written in these hadiths is very difficult to swallow. It is very difficult to believe that a person of such characteristics would become the prophet of more than a billion people. When someone points at how violent Muhammad was, and offers the hadiths as proof, the listener's reaction is of disbelief. The listener feels ashamed and convinces himself that there must be an error somewhere. The natural reaction is to doubt: either the texts that are being quoted are false, or the critic of islam is making it up, or at the very least he is cherry-picking the data among a sea of peaceful, generous and kind actions Muhammad must have taken in his life and which surely explain how so many people follow islam. This is how the first reaction is to convince yourself that these examples are taken out of context.
But everything I am going to quote next are recounts from the islamic tradition itself, taken from the accepted testimonies of the most faithful of Muhammad's followers, and from the writings of the most reputable scholars of islam's faith. When you study these texts carefully you come to realize that the vast majority of Muhammad's actions were violent, and it is the pacific actions that are the exceptions. When you read the Sunnah you realize that it is impossible to affirm that Muhammad was a peaceful man, or that peace is a part of his message. Muhammad's life was filled with cruel episodes.
So, when you read what comes next you do not have to take my word for it or believe me. But do not discard it without searching for evidence on your own. You can look up every single thing I am pasting here, and even read the Sunnah for yourself if you want to satisfy your doubts. You can even look up the biography of Muhammad as written by a reputable islamic scholar such as Al-Tabari, read it, and draw your own conclusions. What follows next is not in any way my opinion, it is a summary of some of the most representative actions that Muhammad took during his life as they appear in muslim texts.
Muhammad was a militar leader that unified the arabic peninsula by forceful conquest. In order to carry out a plan so ambitious he had to assault caravans, siege cities, organize expulsions, destroy temples, massacre and torture entire towns, lapidate hundreds of people, cut out tongues, hands, feet, and heads, burn those who didn't attend prayer alive, order the rape of women, approve of pedophilia, and personally practiced it when he married a 6 year old girl, and imposed an oppressive law on the entire region. By the end of his life he didn't even tolerate the presence of other monotheists as he ordered the expulsion of all jews and christians from the peninsula. Muhammad brought despair and tragedy to every group that rejected his faith and led a life much more violent that what the Qur'an itself stipulates.
Many of the islamic punishments are not written down in the Qur'an but are described in the Sunnah within the hadiths. For example, lapidation of the adulterous does not appear in the Qur'an but does appear several times in the hadiths as it was a practice Muhammad did frequently and as such it comes to be a part of islam morality: lapidating an adulterer is considered to be good and godly within islam.
All of Muhammad actions both the pacific and benevolent ones and the violent, become the moral standard within islam. And these are some of the things that the hadiths describe about Muhammad:
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)." what you know of the Quran (by heart)'
(Bukhari 62:64)
Narrated Anas:
The Prophet cut off the hands and feet of the men belonging to the tribe of 'Uraina and did not cauterise (their bleeding limbs) till they died.
(Bukhari 82:795)
Narrated Abdullah bin Umar:
The Jew brought to the Prophet a man and a woman from amongst them who have committed (adultery) illegal sexual intercourse. He ordered both of them to be stoned (to death), near the place of offering the funeral prayers beside the mosque.
(Bukhari 23:413)
Narrated Abu Qilaba:
Anas said, "Some people of 'Ukl or 'Uraina tribe came to Medina and its climate did not suit them. So the Prophet ordered them to go to the herd of (Milch) camels and to drink their milk and urine (as a medicine). So they went as directed and after they became healthy, they killed the shepherd of the Prophet and drove away all the camels. The news reached the Prophet early in the morning and he sent (men) in their pursuit and they were captured and brought at noon. He then ordered to cut their hands and feet (and it was done), and their eyes were branded with heated pieces of iron, They were put in 'Al-Harra' and when they asked for water, no water was given to them." Abu Qilaba said, "Those people committed theft and murder, became infidels after embracing Islam and fought against Allah and His Apostle.
(Bukhari 4:234)
Narrated 'Abdullah bin Mas'ud:
When the Messenger of God ordered his death, Uqba asked him, 'Who will look after my children, Muhammad?' And the Prophet said: 'Hell!'... [Uqba was] among the most evil of God's servants, the most stubborn, wicked, envious and disbelieving of men and they had been very active in satirizing Islam and its supporters. God damn them! And He did, indeed!
(Bukhari 4:241)
The cases in which Muhammad showed a violent disposition towards other people are numerous. It isn't just a couple of isolated events. The hadiths are filled with events like these. Muhammad approved the assassination of 800 men and children from the tribe of Qurayza that up until that moment had been his allies. Their men murdered an senile woman after they took her prisoner during the assault to the tribe of Banu Hazara. According to Al-Tabari they killed the old woman by tying each foot with a rope to a camel and riding the camels in opposite directions until she was split in half. Right after they gave the woman's daughter to one of the killers for him to rape her.
One could think that in the 7th Century these types of practices were not out of the ordinary and therefore we are analyzing them out of context. But even though royal punishments and torture were not unheard of, in most kingdoms it wasn't a common sight, much less a practice that was applied massively to entire towns of people. Splitting a senile woman in half using camels was in the 7th century something as brutal and cruel as today is tying the body of an enemy to a motorcycle to drag him through the streets of town. And these things happen currently, but the cruelty does not cease to amaze us.
These cruel practices are what allowed islam to expand at such velocity that in less than 30 years it went from being a small group of people fleeing from Mecca into conquering the entire arabic peninsula and converting (or killing) all of its population. Thirty years is what it took. You do not manage a feat like this without a lot of violence.
Muslim morality looks nothing like western morality. Most of the things Muhammad did and taught are in direct conflict with our way of life. But muslims cannot question Muhammad's life like a catholic can question the life of a character in the Bible, but they must take every one of his actions as perfect, infallible, desirable, and noble, even when the practices might shake them for how horrible they are. Islamic morality is above the judgement of man (2:216).
Even if a muslim finds one of Muhammad's violent practices unpalatable or painful, his duty as a muslim is to act according to it. Islamic morality is inflexible, often violent, and does not resemble the 10 Commandments. It differs completely from what we consider good and bad in the West. When a muslim leader talks about goodness or wellness, his idea of it is not the same we have.
I am going to finish her for now and leave the other 2 points (teachings/tradition and practices) for a future post.