Slay the idolaters wherever you find them 9:5
Finding the truth is one's own responsibility, it gives clarity and peace of mind knowing that the causer of life, the creator God is kind and merciful. We have captured various attempts to understand this verse from Qur'aan in its entirety, courtesy of www.islamicity.com and other translation sources. We hope to clarify each such verse that is misunderstood, God willing, one verse at a time over the next few years. Here is the mis-represented verse followed by correct version and various translations.
May God give you the strenght to be a peace maker; that is a conflict reducer and nurturer of Goodwill and harmonious co-existence.
Surah 9, ayah 5, the book says, when the sacred months are over, slay the idolaters wherever you find them. Arrest them, besiege them and lie in ambush everywhere for them."
The Actual Verse
Arabic - Transliteration - Translation (before and after verses) - Notes - 17 Translations.
Qur’aan, Surah 9 -At-Tauba (The Repentance) Verse 5
فَإِذَا انسَلَخَ الأَشْهُرُ الْحُرُمُ فَاقْتُلُواْ الْمُشْرِكِينَ حَيْثُ وَجَدتُّمُوهُمْ وَخُذُوهُمْ وَاحْصُرُوهُمْ وَاقْعُدُواْ لَهُمْ كُلَّ مَرْصَدٍ فَإِن تَابُواْ وَأَقَامُواْ الصَّلاَةَ وَآتَوُاْ الزَّكَاةَ فَخَلُّواْ سَبِيلَهُمْ إِنَّ اللّهَ غَفُورٌ رَّحِيمٌ (9:5)
Faitha insalakha alashhuru alhurumu faoqtuloo almushrikeena haythu wajadtumoohum wakhuthoohum waohsuroohum waoqAAudoo lahum kulla marsadin fain taboo waaqamoo alssalata waatawoo alzzakata fakhalloo sabeelahum inna Allaha ghafoorun raheemun
9:5 And so, when the sacred months are over  , slay those who ascribe divinity to aught beside God wherever you may come upon them,  and take them captive, and besiege them, and lie in wait for them at every conceivable place  ! Yet if they repent, and take to prayer, and render the purifying dues, let them go their way: for, behold, God is much forgiving, a dispenser of grace. 
9:4 But excepted shall be  -from among those who ascribe divinity to aught beside God - [people] with whom you [O believers] have made a covenant and who thereafter have in no wise failed to fulfil their obligations towards you, and neither have aided anyone against you: observe, then, your covenant with them until the end of the term agreed with them.  Verily, God loves those who are conscious of Him.
9:6 And if any of those who ascribe divinity to aught beside God seeks thy protection,  grant him protection, so that he might [be able to] hear the word of God [from thee]; and thereupon convey him to a place where he can feel secure:  this, because they [may be] people who [sin only because they] do not know [the truth].
9:7 HOW COULD they who ascribe divinity to aught beside God be granted a covenant by God and His Apostle,  unless it be those [of them] with whom you [O believers] have made a covenant in the vicinity of the Inviolable House of Worship?  [As for the latter,] so long as they remain true to you, be true to them: for, verily, God loves those who are conscious of Him.
9:8 How [else could it be]?  -since, if they [who are hostile to you] were to overcome you, they would not respect any tie [with you,] nor any obligation to protect [you].  They seek to please you with their mouths, the while their hearts remain averse [to you]; and most of them are iniquitous.
Note 6 :
According to a pre-Islamic custom prevalent in Arabia , the months of Muharram, Rajab, Dhu 'l-Qa'dah and Dhu 'l-Hiijah were considered "sacred" in the sense that all tribal warfare had to cease during those months. It was with a view to preserving these periods of truce and thus to promoting peace among the frequently warring tribes that the Qur'an did not revoke, but rather confirmed, this ancient custom. See also 2:194 and 217.(Quran Ref: 9:5 )
Note 7 : (Quran Ref: 9:5 )
Read in conjunction with the two preceding verses, as well as with 2:190-194, the above verse relates to warfare already in progress with people who have become guilty of a breach of treaty obligations and of aggression.(Quran Ref: 9:5 )
I.e., "do everything that may be necessary and advisable in denotes "any place from which it is possible to perceive The term marsad enemy and to observe his the movements" (Manar X, 199). warfare".(Quran Ref: 9:5 )
As I have pointed out on more than one occasion, every verse of the Qur’an must be read and interpreted against the background of the Qur'an as a whole. The above verse, which speaks of a possible conversion to Islam on the part of "those who ascribe divinity to aught beside God" with whom the believers are at war, must, therefore, be considered in conjunction with several fundamental Qur'anic ordinances. One of them, "There shall be no coercion in matters of faith" (2:256), lays down categorically that any attempt at a forcible conversion of unbelievers is prohibited - which precludes the possibility of the Muslims' demanding or expecting that a defeated enemy should embrace Islam as the price of immunity. Secondly, the Qur'an ordains, "Fight in God's cause against those who wage war against you; but do not commit aggression, for, verily, God does not love aggressors" (2:190); and, "if they do not let you be, and do not offer you peace, and do not stay their hands, seize them and slay them whenever you come upon them: and it is against these that We have clearly empowered you [to make war]" (4:91). Thus, war is permissible only in self-defence (see surah 2, notes 167 and 168), with the further proviso that "if they desist-behold, God is much-forgiving, a dispenser of grace" (2:192), and "if they desist, then all hostility shall cease" (2:193). Now the enemy's conversion to Islam - expressed in the words, "if they repent, and take to prayer [lit., "establish prayer"] and render the purifying dues (zakah)"-is no more than one, and by no means the only, way of their "desisting from hostility"; and the reference to it in verses 5 and 11 of this surah certainly does not imply an alternative of "conversion or death", as some unfriendly critics of Islam choose to assume. Verses 4 and 6 give a further elucidation of the attitude which the believers are enjoined to adopt towards such of the unbelievers as are not hostile to them. (In this connection, see also 60:8-9).(Quran Ref: 9:5 )
Other verses referenced above:
Al-Baqara (The Cow)
2:167 And then those followers shall say: "Would that we had a second chance [in life],  so that we could disown them as they have disowned us!" Thus will God show them their works [in a manner that will cause them] batter regrets; but they will not come out of the fire. 
2:168 O MANKIND! Partake of what is lawful and good on earth, and follow not Satan's footsteps: for, verily, he is your open foe,
2:190 AND FIGHT in God's cause against those who wage war against you, but do not commit aggression-for, verily, God does not love aggressors. 
2:191 And slay them wherever you may come upon them, and drive them away from wherever they drove you away - for oppression is even worse than killing.  And fight not against them near the Inviolable House of Worship unless they fight against you there first;  but if they fight against you, slay them: such shall be the recompense of those who deny the truth.
2:192 But if they desist-behold, God is much-forgiving, a dispenser of grace.
2:193 Hence, fight against them until there is no more oppression and all worship is devoted to God alone;  but if they desist, then all hostility shall cease, save against those who [wilfully] do wrong.
2:194 Fight during the sacred months if you are attacked:  for a violation of sanctity is [subject to the law of] just retribution. Thus, if anyone commits aggression against you, attack him just as he has attacked you - but remain conscious of God, and know that God is with those who are conscious of Him. 
2:256 THERE SHALL BE no coercion in matters of faith.  Distinct has now become the right way from [the way of] error: hence, he who rejects the powers of evil  and believes in God has indeed taken hold of a support most unfailing, which shall never give way: for God is all-hearing, all-knowing.
Al-Mumtahinah (The Examined One)
60:8 As for such [of the unbelievers] as do not fight against you on account of [your] faith, and neither drive you forth from your homelands, God does not forbid you to show them kindness and to behave towards them with full equity:  for, verily, God loves those who act equitably.
60:9 God only forbids you to turn in friendship towards such as fight against you because of [your] faith, and drive you forth from your homelands, or aid [others] in driving you forth: and as for those [from among you] who turn towards them in friendship; it is they, they who are truly wrongdoers!
So if the months the forbidden/sacred ended/passed , so fight/kill the sharers/takers of partners (with God) where/when you found them, and take/punish them and restrict/confine them and remain/be concerned and prepared/beset for them (in) every lookout/observatory , so if they repented, and kept up the prayers and gave/brought the charity/ purification , so free their way/path , that God (is) forgiving, merciful.
But when the forbidden months are past, then fight and slay the Pagans wherever ye find them, an seize them, beleaguer them, and lie in wait for them in every stratagem (of war); but if they repent, and establish regular prayers and practise regular charity, then open the way for them: for Allah is Oft-forgiving, Most Merciful.
Then, when the sacred months have passed, slay the idolaters wherever ye find them, and take them (captive), and besiege them, and prepare for them each ambush. But if they repent and establish worship and pay the poor-due, then leave their way free. Lo! Allah is Forgiving, Merciful.
Then, when the sacred months are drawn away, slay the idolaters wherever you find them, and take them, and confine them, and lie in wait for them at every place of ambush. But if they repent, and perform the prayer, and pay the alms, then let them go their way; God is All-forgiving, All-compassionate.
So when the sacred months have passed away, then slay the idolaters wherever you find them, and take them captives and besiege them and lie in wait for them in every ambush, then if they repent and keep up prayer and pay the poor-rate, leave their way free to them; surely Allah is Forgiving, Merciful.
When the sacred months are over, slay the pagans wherever you find them. Capture, besiege, and ambush them. If they repent, perform prayers and pay the religious tax, set them free. God is All-forgiving and All-merciful.
Once the Sacred Months are past, (and they refuse to make peace) you may kill the idol worshipers when you encounter them, punish them, and resist every move they make. If they repent and observe the Contact Prayers (Salat) and give the obligatory charity (Zakat), you shall let them go. GOD is Forgiver, Most Merciful.
Then when the Sacred Months (the Ist, 7th, 11th, and 12th months of the Islamic calendar) have passed, then kill the Mushrikoon (see V.2:105) wherever you find them, and capture them and besiege them, and prepare for them each and every ambush. But if they repent and perform As-Salat (Iqamat-as-Salat), and give Zakat, then leave their way free. Verily, Allah is Oft-Forgiving, Most Merciful.
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.
When the forbidden months (10,11,12 & 1 of the Islamic calendar) are over, then fight the pagans wherever you find them, seize them, besiege them, and lie in ambush for them in every stratagem of war, but if they repent, establish Salah and pay Zakah, then let them go their way: surely Allah is Forgiving, Merciful.
When the four Sacred Months are over and if the idolaters are still aggressing, neither becoming law-abiding citizens of the State, nor emigrating, subdue them wherever you find them, take them captive, and besiege them, and ambush them. But if they repent from aggression, and help in the consolidation of the Divine System and in setting up the Just Economic Order of Zakat, then leave them free. Verily, Allah is Forgiving Merciful.
So when the sacred months have passed, slay the idolaters, wherever you find them, and take them captive and besiege them and lie in wait for them in every ambush. But if they repent and keep up prayer and pay the poor-rate, leave their way free. Surely Allah is Forgiving, Merciful.
So when the restricted months have passed, then you may kill those who have set up partners wherever you find them, and take them, and surround them, and stand against them at every point. If they repent, and hold the contact-method, and contribute towards betterment, then you shall leave them alone. God is Forgiving, Merciful.
When the sacred months are over, slay the idolaters wherever you find them. Take them and confine them, then lie in ambush everywhere for them. If they repent and establish the prayer and pay the obligatory charity, let them go their way. Allah is Forgiving and the Most Merciful.
And when the months wherein ye are not allowed to attack them shall be past, kill the idolaters wheresoever ye shall find them, and take them prisoners, and besiege them, and lay wait for them in every convenient place. But if they shall repent, and observe the appointed times of prayer, and pay the legal alms, dismiss them freely; for God is gracious and merciful.
And when the sacred months are passed, kill those who join other gods with God wherever ye shall find them; and seize them, besiege them, and lay wait for them with every kind of ambush: but if they shall convert, and observe prayer, and pay the obligatory
And so, when the sacred months are over, slay those who ascribe divinity to aught beside God wherever you may come upon them,' and take them captive, and besiege them, and lie in wait for them at every conceivable place! Yet if they repent, and take to prayer, and render the purifying dues, let them go their way: for, behold, God is much-forgiving, a dispenser of grace .