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I love this story.
First, my usual warning NOT to get distracted by the special effects. Too often modern day preachers spend all their time trying to make the "miracle" seem scientifically plausible, and in effect explain away the significance of the story. Believing in God is already scientifically problematic, so instead of being plausible, invite your congregation to wonder.
Having said that, it is important to know that at the time of Jesus, what happens in this story is NOT that Jesus walks on water. Jesus walks on the sea. And the sea was understood to be a living, chaotic, potentially deadly spirit.
When the disciples see Jesus walking on the sea, they are not relieved, do not shout for joy expecting that Jesus has come to rescue them from the storm (also caused by spirits). Instead, they are terrified. The word used here can also be used to describe a sea that has been agitated and stirred up. In other words, the disciples inner state is now a perfect reflection of their outer circumstances.
They are terrified because they would realize that they are seeing with their human eyes events that can only happen in the realm of the spirits - their first reaction is that they are seeing a ghost. They are terrified because while spirits are everywhere in the human realm, it is deadly for humans to be in the realm of the spirits.
When Jesus immediately says to them, "Take courage, do not be afraid," he is inviting them to have HIS inner state instead of theirs. Walking on the sea is not an idle, capricious, magic trick. After spending time alone in prayer, he has stepped out onto the back of a chaotic and dangerous spirit to go and be with his friends.
What happens next is a poignant testimony of the reality of discipleship, of being a follower of Jesus.
Good old impetuous Peter responds, "Lord, if it is you, command me to come to you." It is important to note that Peter does not act on his own impulse or authority. He asks to be commanded to come to Jesus. He gets out of the boat under the protection of the authority of Jesus. And Peter does not go for a stroll on the sea; he does only what he has been commanded, he comes toward Jesus.
And for a brief few steps, it works! Peter too is able to walk on the back of the chaotic, dangerous spirit, the sea. But as we all know too well, there are many dangers, many distractions. And instead of keeping his focus on Jesus, Peter notices the wind, and the bond with Jesus is weakened.
Notice that Peter BEGINS to sink. That is, Peter is not walking on water. No one BEGINS to sink in water. Try standing on water yourself and see how much time you have to cry out while beginning to sink.
And notice too, that Peter does NOT cry out, "Lord, IF it is you, save me." There are no if's, and's, or but's. Now it is simply, "Lord, save me."
Jesus reaches out his hand and saves Peter. His comment and question to Peter, "You of little faith, why did you doubt," would be better translated as, "You of little trust, why did you hold back?" The issue in this story is not intellectual assent (faith / belief). The issue is loyalty / trust, and not getting distracted in times of trouble and testing.
When they get into the boat, the encounter between Jesus and the spirits of the sea and the wind end; things calm down.
The statement by the disciples, "Truly, you are the Son of God." is simply an affirmation by them of what they witnessed with their eyes: Jesus has shown authority over the spirits of the sea and wind - he is Son of God, since only one of that high a rank in the spirit realm could have authority over the sea and wind.