Effects of Prayer: questions and reflections from Numbers 14

Prayer is an essential part of life. But what does prayer accomplish? This indeed is a fantastic mystery. Scripture is filled with the prayers of many of its central characters. These prayer have different effects. Of course, Scripture abounds with examples of prayers which seem to affect specific circumstances, and prayers which don't. For the most part, I've concluded (I like to think from Scripture) that prayer does not change things, per se. If a small bird can't fall without God's direction, then how can the prayers of a sinful human alter the course of history? With this in mind, I tend to think that perhaps prayer affects situations because God ordains both the ends and means, or perhaps prayer is (mostly) for edifying the person praying.

But then this morning I read Numbers 14. In this passage, the people of Israel become discontent with Moses and Aaron's leadership. God grows angry with the Israelites and shows a desire to simply allow the people go and then begin anew with Moses and Aaron (Numbers 14:1-12). Here's what follows:
Moses said to the LORD, "Then the Egyptians will hear about it! By your power you brought these people up from among them. And they will tell the inhabitants of this land about it. They have already heard that you, O LORD, are with these people and that you, O LORD, have been seen face to face, that your cloud stays over them, and that you go before them in a pillar of cloud by day and a pillar of fire by night. If you put these people to death all at one time, the nations who have heard this report about you will say, 'The LORD was not able to bring these people into the land he promised them on oath; so he slaughtered them in the desert.' "Now may the Lord's strength be displayed, just as you have declared: 'The LORD is slow to anger, abounding in love and forgiving sin and rebellion. Yet he does not leave the guilty unpunished; he punishes the children for the sin of the fathers to the third and fourth generation.' In accordance with your great love, forgive the sin of these people, just as you have pardoned them from the time they left Egypt until now." The LORD replied, "I have forgiven them, as you asked.
Verse 20 shocked me. God seemingly changes his plan because of Moses' intercession. Now, God does punish Israel (He does not allow the entire generation access to the promised land). But what's striking is that he seems to change his will because Moses asked him to.

How does this story (and many others like it) fit with NT teachings that God works everything to fit the purpose of his will (Ephesians 1:11)? Consider Philippians 2, where Paul tells the church that God works in them, both to "will and to work," his own will (12-13). Can we ascertain from this that God works in people to shape and conform their prayers? Or what are we to make of verses such as Matthew 16:18 where Jesus tells Peter that he will build his church, "and the gates of hell will not overcome it?" Clearly the church's growth (in this context) is not contingent on prayer.

I cannot answer this question. I don't know. So what are we to do with dilemmas like this? Isaiah 55:8 tells us that God's ways are not our ways. But this truth should not cause frustration, but cause us to rejoice. We do not have a god who fits our intellectual capacities. Rather, we serve YHWH, triune in nature and perfect in will and action. Taking our example from Paul, may we take pleasure in this mysterious God.

D.A. Carson spoke on this subject in June (2009), answering the question "If prayer changes things, how exactly are we to trust God's sovereignty?" The mp3 (here) is helpful.

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