Praying for peace is good. Praying for justice is good. Praying for your Christian brothers and sisters who are facing torture and death is good. Praying for non-Christians who are facing torture and death is also good. But there is one crucial thing you can pray about that could change the course of history in the Middle East.
Pray that the treacherous actions of ISIS will discredit Islam in the minds and hearts of non-ISIS Muslims to such a degree that they 1) turn away from Islam and 2) open their hearts to the message of Jesus Christ.
You may not know this, but for most men and women who were formerly Muslims but now are followers of Jesus, they came to faith in Christ in two distinct stages, not just one. First, they became disillusioned with Islam. Second, they somehow came in contact with the gospel of Jesus Christ and believed.
The Iranian Christian movement presents the most striking example of what I’m talking about. “On the eve of the 1979 Islamic Revolution in Iran, there were likely no more than 500 Muslim-background followers of Christ in a nation of 40 million mostly Shi’ite Muslims. Three decades later, hundreds of thousands of Iranian Muslims have given their lives to Jesus Christ.” After the rise of the Ayatollah Khomeini and the subsequent imposition of many harsh measures upon his own people, increasing numbers in Iran became disenchanted with Islam. A few of the alienated became atheists. Many continued to self-identify as Muslims, but interpreted Islam in a way that fit their own sensibilities. Astoundingly, tens of thousands came into a personal relationship with Jesus.
Shouldn’t we be praying that the same thing that has been happening in the Persian world (especially Iran) might now happen in the Arab world (including Syria and Iraq)? As followers of Jesus, let’s boldly pray that the straining eyes of those who have been searching for truth in the shadows of Islam will turn away in shame from the men of ISIS who have dedicated themselves to a violent application of the Qur’an. In the name of Jesus, let’s pray that thousands upon thousands of Muslims will be sickened at the sight of the sword so cavalierly wielded in the name of Allah by the adherents of ISIS. Let’s open up the floodgates of heaven in our prayers, asking the Holy Spirit to foster a yearning…and longing…and aching throughout the Middle East for something better than the empty promises of a utopian world under the rule of Islam.
Then let’s pray that those same straining eyes might turn toward the light--the light of the gospel of Jesus Christ. Let’s pray that as these precious people turn away in shame from the violence, they will fix their eyes upon Jesus and find forgiveness and freedom in HIM! Let’s pray that multitudes will be drawn by God’s Spirit into a loving relationship with Messiah Jesus.
So if you’re wondering how to pray about the ISIS crisis in the Middle East, this is one good way to pray.
 David Garrison, A Wind in the House of Islam: How God is drawing Muslims around the world to faith in Jesus Christ (Monument, CO: WIGTake Resources, 2014), 121. I highly recommend this book.