What does God want me to do when he's had an affair, now it's over & he wants to reconcile with me?

Take your time and work things out if you think he is sincere and serious that it was a one time mistake. I have known guys that have made a mistake one time and learned from it and their wife took them back and their relationship was never better. Lay down ground rules though like you will not put up with it a second time cause there is no third chance. And tell him if there is a possibility that you might not trust him enough for awhile that you might 'check on' him until you feel comfortable enough to learn to trust him again and not to hold it against you since he did it to himself.
If your gut feeling is that he did it because he is a womenizer or something you might be better off to tell him to hit the road.

What do you want to do? If he has asked you to forgive him, God would want you to forgive him, that does not mean you should take him back. He has already broken faith in the marriage.
If you love your husband and he is sorry and want you to take him back, you two will need some counseling or you will anyway, becuae the pain of betrayal does not just go away after an apology, he needs to know that too and e willing to deal with it.
If you love and trust your husbands' word enough then take him back, but know it will be hard. If you don't trust that this won't happen again, call it quits.