The opening of Surah 9(Al-Taubah 1-5) is trasnlated as : "“A declaration of the dissolution of agreements from God and His messenger to the idolaters with whom you have made [no-war] agreements. Thus, you [O polytheists] may freely traverse in the land for four months, but know that you shall not escape God’s judgment and that God shall surely humble the unbelievers. A proclamation [should be made] to these people from God and His messenger on the day of Hajj-e-Akbar, [declaring] that God and His messenger are no longer under any obligation toward these polytheists. If you repent, [O polytheists,] it shall be better for you but if you turn your backs [paying no heed], then know that you shall not be able to escape God’s judgment. Give these rejecters the glad tidings of a painful punishment, except those polytheists who have not dishonored their treaties with you and have not aided anyone against you. With these, fulfill your treaties till the appointed term. Indeed, God loves the righteous. When the sacred months are over, slay the polytheists wherever you find them. Arrest them, besiege them and lie in ambush for them.” (Al-Taubah 9:1-5)
A close look at the above verses shall suffice as evidence to the fact that the directive, “Arrest them, besiege them and lie in ambush for them” is given against those polytheists with whom the Muslims, under the leadership of the Prophet (pbuh), had entered into an agreement and who had disregarded this agreement called "Treaty of Huddaibyah" and aided others against the Muslims. Obviously, these qualities cannot be generalized on all the polytheists of the world.Thus, a further qualification of those against whom the directive is given is that besides breaking their oaths with the Muslims, they conspired to banush the Prophet (pbuh) and were the first to attack the Muslims. It is obvious that the referred directive implies to take action against a particular people. It cannot be generalized to the whole world and to all times to come. The Qur’an further clarifies that the directive is mainly against those particular polytheists who were the custodians of the Haram – the Ka`bah
One point to be noted in this Surah 9:5 that those enemies were idolaters(Quraish of Meccah),who wanted war against Muslims and kill the Holly Prophet(pbuh)-even in the Treaty they signed and was written that there would be no more wars.If anyone of you wants more proofs i would send you the Treaty.Anyway,tell me something that what would you expect from a Commander in Chief of an army to do if they are attacked by the enemy-to sit and play chess or play football or relatiate and save themselves?Obviously,it would be to attack and kill the enemies.Thats what Allah asked his Prophet to do in this Surah 9.
I would want to request you guy that if anyone of you doubts about any Verse of Quran should read all the Surah and its Context.Read all the Surah above and believe to see why Allah revealed it to his Prophet and you could better understand the Verse then.