Q. I’m reading in John. Before Jesus walks on water, why do the disciples leave without him? Why would they do that if they were following him? Do you think he told them, “If I’m not down from the mountain by tonight, go on ahead to Capernaum without me?”
John’s gospel says simply, “When evening came, his disciples went down to the lake, where they got into a boat and set off across the lake for Capernaum. By now it was dark, and Jesus had not yet joined them.” This does make us wonder what kind of arrangements Jesus had made with his disciples beforehand.
But Mark and Matthew shed more light on this question in their accounts of this day in the life of Jesus, which included the feeding of the 5,000 and then Jesus walking on the water to join the disciples in the boat. Mark explains that “it was late in the day” even before the large crowd was fed, so that once everyone had eaten, “Immediately Jesus made his disciples get into the boat and go on ahead of him to Bethsaida, while he dismissed the crowd. After leaving them, he went up on a mountainside to pray.” (They were on the “far shore of the Sea of Galilee” according to John, so Bethsaida and Capernaum were in the same general direction from there; either city could be used to describe the boat’s general heading.) Matthew says something very similar to Mark about why Jesus stayed behind. So it appears that there was some urgency to get the group to its next destination, enough so that Jesus sent the disciples on ahead while he wrapped things up on the “far shore” and then spent some time in prayer, before taking his extraordinary route to rejoin the disciples!
That is likely the reason for the separate departures. But perhaps more significant for our understanding of this day in the life of Jesus is the theological motif that John brings out as he tells the story. As I explain in my study guide to John, in that gospel, “the festivals and locations that Jesus visits allow his identity to be disclosed against the symbolic background of Jewish religious life and history.” In this particular case:
The fourth section of the Book of Signs describes a journey that Jesus takes across the Sea of Galilee and back. The action occurs at the time of Passover. But in this section Jesus’ identity is still not explored against the background of that festival. (This will happen in the Book of Glory.)
Instead, the focus is on the event that Passover commemorates: the exodus of the people of Israel from Egypt under the leadership of Moses. Jesus’ identity is explored in this section against the background of that event. While Jesus is on the far shore of the lake, he miraculously feeds a large crowd. When the crowd returns to the opposite shore, they compare this feeding with the manna, the “bread from heaven,” that Moses gave the Israelites in the wilderness. And to get back across the lake himself, Jesus miraculously walks on the water. This recalls the way God made a path through the Red Sea so the Israelites could escape from the Egyptians. The two “signs” that Jesus does at the beginning of this section thus associate him with the exodus.
So we might say that the reason for the disciples leaving ahead of Jesus was the demands of the group’s ministry schedule and responsibilities. But in the larger plan of God, the purpose for them leaving earlier, occasioning Jesus’ walk on the water, was to reveal more of his identity and glory, as happens throughout the gospel of John.
Good Question 
I think there’s more. It goes back to John Ch. 6. Jesus has already gone up to Jerusalem to the sheep market, to the pool, called Bethesda (Ch. 5), that an angel would sometimes stir the water, and whoever was first to enter, that person would be healed. It’s there Jesus approaches the cripple who he knows has been waiting by this pool, this way, as a cripple for a long time..almost 4 decades (38 yrs) (Ch.5 V.5.) and Jesus comes directly to him without revealing to the man who he is and asks “Wilt thou be made whole?” and the man provides the same truth Adam provided God in Genesis, after he either deliberately ate or Eve deliberately mixed in w/his food, the cripple simply states because he is without help by another man when he tries to enter, always another crippled or infirmed steps over or in front of him and gets healed before him nstead. Jesus simply responds to this reply, “Rise, take up they bed, and walk” – that there isn’t any other man, but Jesus and him, a cripple, simply doing what Jesus said…from a condition that bound him for decades that was impossible to be done on his own, or by the help of any man, or on himself alone to do. He’s instantly made whole, and the Pharisees see him carrying his bed and either escort him or he goes on his own to the Synagogue, as it’s the Sabbath exactly in the condition Jesus told him to be in (risen, carrying his bed, and walk) Reading on, this command of Jesus, since he owns the Sabbath, commanded him on that day to do it as part of his healing. We see later how Jesus tells the Pharisees, why, that he simply does he’s seen his Father do, and has the power and authority to do it; but, it’s the Pharisees that don’t believe him, just like they didn’t believe Moses, as Moses also testified of him. This above, Jesus healing those infirmed, is reason why a great multitude followed Jesus out to sea as he crossed the Sea of Galilee. When they get to the other side, it’s when Jesus “proves” Philip by asking “Whence shall we buy bread, that these may eat?” John Ch.6 V.5 – when they’re out well across the sea near the mountains and too far away from anyplace for any market, or any amt of money they have to pay for such a crowd to eat. The scripture says “Passover was at nigh” (V.4) meaning it was about to begin, and after Philip’s reply, Andrew tells Jesus there’s a lad with 5 barley loaves and 2 fish (meal for 1–a kid), and with that, Jesus feeds a multitude of men greater than 5000. The amazing thing is, just like with the cripple, instead of telling Philip what Phillip expects, (go someplace impossible & buy food…which is impossible, but what Philip as a man in his flesh could attempt anyway), he tells all the disciples to “have the men be seated.” That’s an action that doesn’t make any food. Since there’s a “lad” present, or a small boy, there had to be other children, women even….a whole crowd of others besides men, but Jesus has the disciples have the men be seated, as if to a meal, even when there isn’t any food yet, just like the cripple earlier wasn’t made whole yet, when Jesus approached him and talked with the cripple. He already knows he’s going to heal the cripple, just as he already knew he was going to feed this crowd of 5000. The miracle is as is said. He fed all with 5 barley loaves, and 2 fish enough that all were completely satiated, and afterward, Jesus commands the disciples to collect all remaining leftovers so “nothing be lost.” …so that even the food of the miracle wouldn’t be lost. (V. 12) and that collected was 12 full baskets. A full basket for each of the disciples who distributed the food after Jesus blessed it. It’s after this, these two miracles (cripple earlier, and Jesus feeding the 5000) that his disciples “realize” Jesus is just like what happened with the prophets, like Joshua and Moses earlier, and were going to make him King by force – Jesus perceived they were going to do this, so he left them and went into another mountain alone. It’s after Jesus does this and doesn’t come back that the disciples do what Jonah did. They don’t wait on Jesus, they leave on their own and hire their own boat to go back to Capernaum without any King to defeat the Romans with and take back their holy land by force and thru miracles Jesus could do–they thought that’s how the kingdom of Israel would be restored, like it was in the Old Testament. When Jesus, just like with Jonah says “Not by might, nor by power, but by my spirit” does his reign as King from Jerusalem over the whole earth, that God himself will accomplish it, without any help from men or thru the work of flesh. He’s going to reign over the whole earth, and it will be just as Zachariah prophesied, that men in his reign will pray for rain, he he will form them as men ask, as all the nations are turned to him, and in that day, even the moon and the sun will be ashamed because Jesus who created them will be on earth and his light is greater than these mere creations. Amen and AMen