First of all, we should pray for our own heart. It is too easy to have a hard heart, and say, "Let's just blast them to bits." God has called us to "Love our enemies..." God created the people involved in ISIS; they are made in his image. All people are valued by God, even when they do anti-God-like acts, and all people do anti-God-like acts. If we allow our hearts to become hard, we most likely will allow hardness of heart in other relationships and other areas of life.
As we pray for our own heart, we should "take the log out of our own eye." If we are abusive to people, how can we condemn their abusiveness. If we entertain ourselves with violence, how can we condemn their violence. We ought to ask God's Spirit to reveal to us anything that creates a lack of peace in our lives.
Secondly, we should pray for the people of ISIS. Let me list a few ways to pray for the individuals of ISIS:
1) Pray for repentance. Pray that they will see the evil of their ways and turn from them. Most Muslims say that ISIS is doing evil according to the Islamic faith, much less in comparison to Jesus Christ. Just as the apostle Paul, who persecuted Christians had a conversion (Acts 9) and became a Christian himself, so too many of the people of ISIS could experience conversion.
2) Similarly, but using different words, pray that God will deliver them from the power of Satan to God. Their struggle, and our struggle also, is not with flesh and blood, but the spiritual forces of evil that dominate and rule them and the world. In other words, they and we are in the midst of a spiritual war. Currently, they are fighting along with Satan. We want God to deliver them.
3) Pray that God will restrain their evil and violence. However, God does it, ask God to intervene and prevent needless deaths and bloodshed.
4) Pray that people will not be attracted to ISIS. ISIS grew out of a complex situation which I don't totally understand. Many of the people were facing poverty, unemployment, a barren land, and a political vacuum. (The U.S. weakened the government of Iraq through its invasions, and the nation of Syria is involved in a civil war.) People stuck in despair are finding hope and a sense of belonging in ISIS. As I read about this, it sounds like the same reasons people enter into gangs.
Thirdly, we should pray for the world leaders. They need wisdom to know how to respond to this complex and confusing issue. Pray that their eyes will be opened to the truth. Pray that our own world leaders will:
1) repent of their decisions that led to ISIS or are even currently supporting ISIS
2) not be blinded by their own ideas but understand the prophecies of Islam. I write this because an ISIS supporter wrote to Graeme Wood, who wrote a long article in The Atlantic about the beliefs of ISIS, and this is just one sentence of his response, "The enemies of the Muslims may be aware of what the Muslims are planning, but it won't benefit them at all as they prefer to either keep their heads in the sand, or to fight their imaginary war based upon rational freedom-loving democrats vs. irrational evil terrorist madmen."
3) work together as a whole to create a "comprehensive, multilateral strategy" to respond to ISIS and all the issues of the Middle East.
Fourthly, we should pray for the victims and their families and their communities in which ISIS exists. Pray that:
1) God will provide spiritual strength for the victims as they face death or slavery or imprisonment. Pray that they will turn to Jesus and find strength in him.
2) the families and communities will find comfort in God. Pray that they will experience God's wholeness in the midst of this brokenness.
3) God will provide the resources needed for both the refugees and those still "trapped" by ISIS.
Fifthly, pray that God will raise up peacemakers of which the church of Jesus Christ is to be. Pray that we, as the church of Jesus Christ, will be responsive to God's Spirit in trying to minister in this situation. Pray for organizations like MCC who are trying to minister to the refugees of not only the Syrian civil war but also ISIS.
Finally, in some form, pray that God's glory will be seen through this crisis.