The Verses about the war in Quran are deviated from their meaning deliberately by some non-believers. The meaning of the verses are intended to be interpreted apart form their context. However, if those verses were interpreted within the general logic of Quran and within the context of the topic; verses would be easily clarified. The verse in Surat al Tevbe is as follows:
“Fight those who believe not in Allah nor the Last Day, nor hold that forbidden which hath been forbidden by Allah and His Messenger, nor acknowledge the religion of Truth, (even if they are) of the People of the Book, until they pay the Jizya with willing submission, and feel themselves subdued.” ( Surat-al Tevbe, 29)
If we closely examine the verse, people with whom it is ordered to make war are not the all the people of the Book. The reason it is ordered to fight with them is that they started the war in the first instant. If the Surat-al Tevbe were read from the beginning; the subject would be understood more.
All the verses about the war in Quran should be evaluated within the integrity of whole Quran. On the contrary to all claims; war is allowed only in case of self-defense in Quran. A war declared just for conquering other countries is not a religious war according to Quran. Throughout the history, some Islamic states declared wars to some countries for invasion but those wars couldn’t be regarded as religious wars but political wars instead because such a war just for invasion is not acceptable by Allah. In Surat-al Baqara Allah says like this :
(2:190-193) Fight in the cause of Allah those who fight you, but do not transgress limits; for Allah loveth not transgressors. And slay them wherever ye catch them, and turn them out from where they have Turned you out; for tumult and oppression are worse than slaughter; but fight them not at the Sacred Mosque, unless they (first) fight you there; but if they fight you, slay them. Such is the reward of those who suppress faith. But if they cease, Allah is Oft-forgiving, Most Merciful. And fight them on until there is no more Tumult or oppression, and there prevail justice and faith in Allah. but if they cease, Let there be no hostility except to those who practise oppression.
As we can understand from those verses; war can be declared against only those who declare war first. Moreover, Allah warns believers not to transgress the limits in this war. During the war, if the other party cease to fight and ask for mercy ; Muslims should obey this and cease the war as well. For the damage they get from war, they ask for “Cizye”; this Arabic word is conjugated from the word Punishment in Arabic ; hence means “ War compensation” not he tax. War compensation is the proof for war is not for invasion in Quran. Because if the war were for invasion only ; the war compensation would not be demanded. The main aim for invasion is to gather the other people’s land; asking for the damage of the war would be meaningless. It is war compensation, which Savage Germany paid after World War 2. Cizye, war compensation, exists in Civil Law as well.
We have seen in above verses that war is only in case of self-defense. Allah demands from Muslims fight back with all their power when they are under attack for the first time. Related verses in Surat-al Tvebe are as follows:
(9:13-15) Will ye not fight people who violated their oaths, plotted to expel the Messenger, and took the aggressive by being the first (to assault) you? Do ye fear them? Nay, it is Allah Whom ye should more justly fear, if ye believe! Fight them, and Allah will punish them by your hands, cover them with shame, help you (to victory) over them, heal the breasts of Believers, And still the indignation of their hearts. For Allah will turn (in mercy) to whom He will; and Allah is All-Knowing, All Wise.
It is obvious that being steady and hard in the war will maintain war to finish earlier and would be a demotivation sample for future wars. To counter attack to those first aggressors and make them feel regret about their transgression would be the most reasonable way to protect peace.
Apart form these, Allah permits war for the protection of weakened Muslims, the ones under oppression and the ones in deep need.
(Women 4:75 ) And why should ye not fight in the cause of Allah and of those who, being weak, are ill-treated (and oppressed)?- Men, women, and children, whose cry is: “Our Lord!
Rescue us from this town, whose people are oppressors; and raise for us from thee one who will protect; and raise for us from thee one who will help!”
Such a war would be not for violence but for the mercy for the weak people. Islam, which is against cruelty, advice believers to serve as a protector and mercy showing people for people under oppression. And in case of peace; Allah orders believers to be just and good. The aim here is to keep peace continuity against war.
(Examining her ,60:8) Allah forbids you not, with regard to those who fight you not for (your) Faith nor drive you out of your homes, from dealing kindly and justly with them: for Allah loveth those who are just.
Whichever religion has the other party confronting believers, if they want to live in peace; approach of believers towards this could be only friendly approach as per Quran. Consequently, if those verses are read as a whole and interpreted as a whole, there is no contradiction among them at all.