According to the Koran, war represents an "unwanted obligation" which has to be absolutely carried out with strict observance of particular humane and moral values and resorted only when it is inevitable.
In a verse, it is explained that those who start wars are the disbelievers and that God does not approve wars:
…Each time they kindle the fire of war, Allah extinguishes it. They rush about the earth corrupting it. Allah does not love corrupters. (Surat al-Ma'ida: 64)
A closer examination of Prophet Muhammad's life reveals that war is a method resorted for defensive purposes only in unavoidable situations.
The revelation of the Koran to Prophet Muhammad lasted for 23 years. During the first 13 years of this period, Muslims lived as a minority under a pagan rule in Mecca and faced much oppression. Many Muslims were harassed, abused, tortured, and even murdered, their houses and possessions were plundered. Despite this however, Muslims led their lives without resorting to any violence and always called pagans to peace.
When the oppression of pagans escalated unbearably, Muslims emigrated to the town of Yathrib, which was later to be renamed Medina, where they could establish their own order in a more friendly and free environment. Even establishing their own political system did not prompt them to take up weapons against aggressive pagans of Mecca. Only after the following revelation, the Prophet commanded his people to get prepared for war:
Permission to fight is given to those who are fought against because they have been wronged - truly God has the power to come to their support - those who were expelled from their homes without any right, merely for saying, 'Our Lord is God'… (Surat al-Hajj: 39-40)
In brief, Muslims were allowed to wage war only because they were oppressed and subjected to violence. To put it in another way, God granted permission for war only for defensive purposes. In other verses, Muslims are warned against use of unnecessary provocation or unnecessary violence:
Fight in the Way of God against those who fight you, but do not go beyond the limits. God does not love those who go beyond the limits. (Surat al-Baqara: 190)
After the revelations of these verses, wars occurred between Muslims and pagan Arabs. In none of these wars, however, were the Muslims the inciting party. Furthermore, Prophet Muhammad established a secure and peaceful social environment for Muslims and pagans alike by signing a peace agreement (Hudaybiya) which conceded to the pagans most of their requests. The party who violated the terms of the agreement and started a new war was again the pagans. However, with rapid conversions into Islam, the Islamic armies attained great power against the pagan Arabs and Prophet Muhammad conquered Mecca without bloodshed and in a spirit of tolerance. If he willed, he could have taken revenge on pagan leaders in the city. Yet, he did not do harm to any one of them, forgave them and treated them with the utmost tolerance. Pagans, who would later convert to Islam by their own will, could not help admiring such noble character of the Prophet.
The Islamic principles God proclaims in the Koran account for this peaceful and temperate policy of Prophet Muhammad. In the Koran, God commands believers to treat even the non-Muslims kindly and justly:
...God does not forbid you from being good to those who have not fought you over religion or driven you from your homes, or from being just towards them. God loves those who are just. God merely forbids you from taking as friends those who have fought you over religion and driven you from your homes and who supported your expulsion... (Surat al-Mumtahana: 8-9)
The verses above specify the outlook of a Muslim on non-Muslims: A Muslim should treat all non-Muslims kindly and avoid making friends only with those who show enmity to Islam. In case this enmity causes violent attacks against the existence of Muslims, that is, in case they wage a war against them, then Muslims should respond them justly by considering the humane dimensions of the situation. All forms of barbarism, unnecessary acts of violence and unjust aggression are forbidden by Islam. In another verse, God warns Muslims against this and explains that rage felt for enemies should not cause them to drift them into injustice:
You who believe! Show integrity for the sake of God, bearing witness with justice. Do not let hatred for a people incite you into not being just. Be just. That is closer to heedfulness. Heed God (alone). God is aware of what you do. (Surat al-Ma'ida: 8)
The Meaning of the Concept of "Jihad"
Another concept that deserves clarification due to the content of this article is the concept of "jihad".
The exact meaning of "Jihad" is "effort". That is, in Islam, "to carry out jihad" is "to show efforts, to struggle". Prophet Muhammad explained that "the greatest jihad is the one a person carries out against his lower soul". What is meant by "lower soul" here is the selfish desires and ambitions. A struggle given on intellectual grounds against anti-religious, atheist views is also a form of jihad in its complete sense.
Apart from these ideological and spiritual meanings, struggle in the physical sense is also considered as "jihad". However, as explained above, this has to be a struggle carried out solely for defensive purposes. The use of the concept of "jihad" for acts of aggression against innocent people, that is for terror, would be unjust and a great distortion.
Compassion, Tolerance and Pacifism in Islam
To state briefly, the Islamic political doctrine is extremely peaceful and moderate. This fact is also confirmed by many non-Muslim historians and theologians. One of these is the British historian, Karen Armstrong, a former nun and a renowned expert on Middle East history. In her book, Holy War, in which she examines the history of the three great divine religions, she comments:
... The word Islam comes from the same Arabic root as the word peace and the Koran condemns war as an abnormal state of affairs opposed to God's will: "When the enemies of the Muslims kindle a fire for war, Allah extinguishes it. They strive to create disorder in earth, and Allah loves not those who create disorder." (Koran 28:78). Islam does not justify a total aggressive war or extermination, as the Torah does in the first five books of the Bible. A more realistic religion than Christianity, Islam recognizes that war is inevitable and sometimes a positive duty in order to and oppressions and suffering. The Koran teaches that war must be limited and be conducted in as humane a way of possible. Mohammed had to fight not only the Meccans but also the Jewish tribes in the area and Christian tribes in Syria who planned on offensive against him in alliance with the Jews. Yet this did not make Mohammed denounce the People of the Book. His Muslims were forced to defend themselves but they were not fighting a holy war against the religion of their enemies. When Mohammed sent his freedman Zaid against the Christians at the head of a Muslim army, he told them to fight in the cause of God bravely but humanely. They must not molest priests, monks and nuns nor the weak and helpless people who were unable to fight. There must be no massacre of civilians nor should they cut down a single tree nor pull down any building. This was very different from the wars of Joshua. 
Following the death of Prophet Muhammad, Muslims continued to treat the members of other religions with tolerance and respect. Islamic states became the secure and free home of both Jews and Christians. After the conquest of Jerusalem, Caliph Omar calmed the Christians who were in fear of a massacre and explained to them that they were secure. Furthermore, he visited their churches and declared that they could continue to practise their worship freely.
In 1099, 4 centuries after the conquest of Jerusalem by Muslims, Crusaders invaded Jerusalem and put all Muslims inhabitants to the sword. Again, contrary to the fears of Christians, Saladin, the Muslim general who captured Jerusalem and saved the city from invasion in 1187, did not touch even a single civilian and did not allow a single soldier to plunder. Moreover, he allowed the invading Christians to take all their possessions and leave the city in security.
The periods of Seljuk Turks and the Ottoman Empire were also marked by the tolerance and justice of Islam. As is known, Jews who were expelled from Catholic Spain found the peace they sought on the lands of Ottoman Empire, where they took refuge in 1492. Sultan Mehmed, the conqueror of Istanbul, also allowed Jews and Christians religious freedom. Regarding the tolerant and just practises of Muslims, historian A. Miquel states the following:
The Christians were ruled by a very well administered state which was something that did not exist in the Byzantium or Latin sovereignty. They were never subjected to a systematized oppression. On the contrary, the Empire, and foremost Istanbul, became a refuge for the much tortured Spanish Jews. They were never forced to accept Islam. 
John L. Esposito, a professor of Religion and International Politics at the Georgetown University, makes a similar comment:
For many non-Muslim populations in Byzantine and Persian territories already subjugated to foreign rulers, Islamic rule meant an exchange of rulers, the new ones often more flexible and tolerant, rather than a loss of independence. Many of these populations now enjoyed greater local autonomy and often paid lower taxes... Religiously, Islam proved a more tolerant religion, providing greater religious freedom for Jews and indigenous Christians. 
As is clarified in these words, history never witnessed Muslims as "makers of mischief". On the contrary, they brought security and peace to the people from all nations and beliefs inhabiting the large territory over which they reigned. (For further reference, see Justice and Tolerance in the Koran, by Harun Yahya, 2000)
In brief, compassion, peace and tolerance constitute the very basis of the values of the Koran and Islam aims to wipe mischief out of the earth.
The commands of the Koran and the ways Muslims practised them throughout history are so clear as to leave no room for dispute.
1- Karen Armstrong, Holy War, MacMillian London Limited, 1988, p. 25
2- Feridun Emecen, Kemal Beydilli, Mehmet Ýpþirli, Mehmet Akif Aydýn, Ýlber Ortaylý, Abdülkadir Özcan, Bahaeddin Yediyýldýz, Mübahat Kütükoðlu, Osmanlý Devleti Medeniyeti Tarihi, (The History of the Ottoman State), Istanbul: 1994, Ýslam Tarih, Sanat ve Kültür Araþtýrma Merkezi, p. 467
3- John L. Esposito, The Islamic Threat: Myth or Reality, Oxford University Press, New York, 1992, p. 39