Examination of Verse 5 of Surat at-Tawba:
In order to understand the conditions in the above verse we need to start reading from verse 1 of Surat at-Tawba; in that way we see that the polytheists deserving to be counter-attacked are not “all polytheists” but those perpetrating savage attacks on Muslims and who then come to agreements in order not to fight during the sacred months. The polytheists here are the ones who have cunningly tried to hunt Muslims down and have continued to attack them during the sacred months and have taken Muslims’ lives, although they have made a fair agreement with Muslims and they very well knew that Muslims would not get into a war during the sacred months.
Under these conditions, Muslims are given the right in this verse to defend themselves against savage attacks. As shown in the verse, although the polytheists carried out their savage attacks in the sacred months, Muslims did not respond during those months, as commanded by God. They exhibited patience during those months and only began counter-attacking once the sacred months were over. We also see that the verse describes the method that needs to be adopted in defense: seizure, siege and lying in wait on all roads. The primary conditions in wars based on international law are siege and seizure. The passages required for the siege are taken and held and the other side is thus prevented from moving. This verse therefore described the method adopted and now regarded as legitimate under international law. The only difference is that it is not Muslims doing the attacking; they are simply trying to put an end to the attacks against them.
In verse 6 of Surat at-Tawba, Muslims are told to help an idolater who seeks shelter with them and asks for their help, even at the cost of endangering their own lives.
There is also no question in this verse of engaging in any fight against those who stop their attacks and repent. They must be released; that is explicit.
When we look at the very next verse, we find a very important statement that describes the loving and protective spirit of the Qur’an. This verse eliminates all the claims made about Muslims by the opponents of Islam. The verse reads:
If any of the polytheists ask you for protection, give them protection until they have heard the words of God. Then convey them to a place where they are safe. That is because they are a people who do not know. (Qur'an, 9:6)
Through this verse, Muslims are advised to help a polytheist who has taken shelter with them and seeks their help, even if that endangers their own lives. The verse even suggests that such a Muslim should use himself as a shield to protect such polytheists. To put it another way, he has a responsibility to risk his own life to protect someone who denies God and to carry him to safety.
This is what the Qur’an commands. According to that commandment, someone is not to be killed for not believing in God. On the contrary, he must be protected, even at the cost of Muslims’ lives. Therefore, the justification for war has nothing to do with whether the other side believes in God or not or belongs to another faith. The justification for war is that the other side engages in assaults and torture, and takes people’s lives.
Another fact set out in the verse is that all people must be under the protection of Muslims so long as they do not attack or engage in extreme behavior, irrespective of their religion, language, ethnicity or beliefs. A Muslim has a responsibility to protect the People of the Book, or even an atheist or a communist, in the same way that he does other Muslims; this is a requirement of being a Muslim; this is the description of a Muslim in the Qur’an. If someone says, “I am a Muslim,” he must be protective of others.