The obvious lesson that the disciples learned from this experience was that Jesus was the divine Son of God. Mark tells us that they did not make this deduction when they had participated in the feeding of the five thousand (Mark 6:51-52). Now they had seen Jesus do something incredible and they confessed that he was the Son of God. Perhaps it is the case that we are better spiritual scholars in dark times than we are in situations when things are going well.
It may also be the case that they heard Jesus say an incredible comment about himself. The words translated ‘It is I’, which Jesus used to comfort his disturbed disciples, are literally ‘I am’, which when taken literally are a claim to deity. Whether they understood his words that way cannot be known, although we can see how they are an indication of his deity. It is important to recognise that whenever Jesus draws near to help us, he does so as the eternal God.
Once they were back together in the boat, the focus was not on Peter and his unusual experience. Instead of expressing curiosity to Peter about how he felt after his time on the water, they all (including Peter) focussed on saying to Jesus that he was the Son of God. Peter went through an incident in which he discovered what Jesus could do for a struggling disciple, but the overall consequence was that all of the disciples discovered more about Jesus.
So they reached the other side with Jesus, even if for most of the journey he was absent from the boat. Yet his eye was continually on them even although they could not see him until he drew near to them. And it is the same with us if we are depending on him. He arranges our providences, he sees us through those providences, and he will be us when each providence comes to a close.