The presence of God in darkness in the New Testament is vitally important to our understanding of our mystical relationship with God.
"While he was still speaking, suddenly a bright cloud overshadowed them, and from the cloud a voice said, ‘This is my Son, the Beloved; with him I am well pleased; listen to him!’ When the disciples heard this, they fell to the ground and were overcome by fear. But Jesus came and touched them, saying, ‘Get up and do not be afraid.’ And when they looked up, they saw no one except Jesus himself alone" ( Matthew 17:5-8; emphasis added).
"Then a cloud overshadowed them, and from the cloud there came a voice, ‘This is my Son, the Beloved; listen to him!’ Suddenly when they looked around, they saw no one with them anymore, but only Jesus" (Mark 9:7-8; emphasis added).
"Just as they were leaving him, Peter said to Jesus, ‘Master, it is good for us to be here; let us make three dwellings, one for you, one for Moses, and one for Elijah’—not knowing what he said. While he was saying this, a cloud came and overshadowed them; and they were terrified as they entered the cloud. Then from the cloud came a voice that said, ‘This is my Son, my Chosen; listen to him!’ When the voice had spoken, Jesus was found alone. And they kept silent and in those days told no one any of the things they had seen" (Luke 9:33-36).
The darkness spoken about in these passages from the Synoptic Gospels seem to come from two words: “cloud” and “overshadow” (from the Greek word επισκιάζω [episkiazw]). They set up a juxtaposition with the narrative of light so prevalent in the Transfiguration. Here's what I mean:
The Transfiguration demonstrates and confirms the divinity of Jesus: (1) Jesus shines with light, (2) God the Father tells the Apostles that Jesus is His Son; (3) the experience of light foreshadows the future glory of Jesus; (4) the presence of Moses represents the importance of the law (and that Jesus surpasses those who gave it); (5) the presence of Elijah represents the importance of prophecy (and that Jesus fulfills it); and (6) the combined presence of Moses and Elijah represents the communion of saints, which glorifies Jesus unceasingly.
In comparison, the narrative of “cloud” or “overshadowing” in the Transfiguration demonstrates and confirms for man that he shares in the life of the Trinity: (1) when Peter, James, and John physically see Christ illumined (along with Moses and Elijah) Peter offers to set up three tabernacles (at one level this demonstrates that man can enter into the Holy of Holies, but only after they understand that the light of God is not a purely physical thing [as Peter did]; (2) the presence of the bright cloud that overshadows Peter, James, and John indicates the presence and work of the Holy Spirit in the life of man (the “bright cloud” occurs in Matthew 17 and is more often associated with the presence of the Holy Spirit; see St. Jerome Homily 80, et. al.); (3) Peter, James, and John hear the voice of the Father in a cloud, meaning that man was created by and invited to return to the Father who is in heaven; (4) the experience of the cloud that is not bright (in Mark 9 and Luke 9 there is no indication that it is a “bright” cloud) demonstrates that man is called to know He who is unknowable (i.e., union with the Most Holy Trinity); (5) the experience of the dark cloud also demonstrates the distance between man and God; (6) being able to see Moses in this experience not only demonstrates the importance of the law of God, but also the ascent of the spiritual life [see The Life of Moses by St. Gregory of Nyssa]; (7) being able to physically see Elijah not only reiterates the importance of the prophets of God, but also calls to mind the need for each Baptized Christian to be a herald for Christ; and (8) the presence of both Elijah and Moses is an invitation to become a saint in this world by believing in and living for Christ.
After analyzing the Transfiguration texts, then, what seems to emerge is that the light refers to the divinity of Christ, the bright cloud refers to the presence and work of the Holy Spirit; and the dark cloud represents the energies of God. This analysis becomes even more interesting when one considers the Annunciation narrative as well.
"And the angel answered and said to her, ‘The Holy Spirit will come upon you, and the power of the Highest will overshadow you; therefore, also, that Holy One who is to be born will be called the Son of God’" (Luke 1:35).
The account we have in Luke seems to offer a similar track to that of the Transfiguration: (1) the Holy Spirit will come upon Mary (not unlike the bright cloud did in the Transfiguration for Peter, James, and John in the Matthean account); (2) the power of God the Father will overshadow Mary (not unlike the cloud that overshadows Peter, James, and John in the Markan account); and (3) Jesus, who is the Christ, is the Holy One who will bring the light of salvation to the world (not unlike the light that Peter, James, and John experienced with the illumined Jesus.
It is quite interesting to note here that Mary, Peter, James, and John were all transfigured by the cloud too. So much so, in fact, that Peter’s shadow was strong enough to heal the sick.
"Now many signs and wonders were done among the people through the apostles. And they were all together in Solomon’s Portico. None of the rest dared to join them, but the people held them in high esteem. Yet more than ever believers were added to the Lord, great numbers of both men and women, so that they even carried out the sick into the streets, and laid them on cots and mats, in order that Peter’s shadow might fall on some of them as he came by. A great number of people would also gather from the towns around Jerusalem, bringing the sick and those tormented by unclean spirits, and they were all cured" (Acts 5:12-16).
Therefore, the experience of Mary and the Apostles was not unlike what Moses experienced in Exodus: they became transfigured humans on earth. So let us pray for each other that we may have the faith and the courage to enter the cloud.