In our Christian life, we encounter light (see “You Are Light“) – and also darkness. But take note: there is more than one kind of darkness. There is a darkness that is not from God, the darkness of evil and sin. This darkness we want to avoid like the plague.
And there is a darkness that is in reality light, but in our limited perception, it seems dark to us. This is a darkness that is as necessary for our growth and spiritual health as nighttime darkness is necessary for some plants to bloom.
This we may call a blessed darkness, a holy darkness.
It may be experienced simply as not being able to see or understand, because we are human 
and the realm of God is the realm of Holy Mystery. While God is closer to us than we are to ourselves, God is also Other. God is not like us. “My thoughts are not your thoughts,” God tells us, “nor are your ways my ways” (Isaiah 55:8). Sometimes we are given the grace to see how God is working in our lives and to experience in our prayer the light of God’s presence. But often we can’t see.
One form of this darkness is the experience of waiting on God.
We see an important example of this near the end of the Easter season, after the Ascension of Jesus into heaven. For a time, the disciples and friends of Jesus, along with Mary his mother, must wait in holy darkness.
Jesus has left them. At least it seems that way. Luke tells us in the first chapter of Acts that “a cloud took him out of their sight.” Before leaving, Jesus had cautioned his disciples “not to leave Jerusalem, but to wait there for the promise of the Father.” So they go to the Upper Room, the Cenacle, and pray together. They don’t know what they are supposed to do otherwise. They don’t know what their mission is to be. They don’t know how they are supposed to deal with the lack of Jesus’ visible presence in their lives.
This is the holy darkness of waiting in prayer. It means waiting in total dependence on God, since they are helpless on their own to bring about that for which they long. This is the blessed darkness of Mystery, an obscurity that in reality is the Light and presence of Christ in newness, though experienced as absence and as emptiness and as unknowing, because it can’t yet be perceived until the outpouring of the Spirit at Pentecost.
There is a necessary waiting that brings us face to face with our own weakness and need and desire for God, and with the fact that we can’t control God or save ourselves. It is a waiting that removes our conceit, along with any pride in our spiritual experiences. We then accept the obscurity of this prayer as sacred, for when we are truly waiting on God, the unknowing that feels like darkness is filled with the invisible light of Christ.
God is light, and in him there is no darkness at all.
(1 John 1:5)