15 When Jesus therefore perceived that they would come and take him by force, to make him a king, he departed again into a mountain himself alone.

[Take him by force, to make him a king] The Jews had often suffered by famine in those times in which their enemies were permitted to prevail over them; but, finding that Jesus had such power as to multiply a few loaves to feed thousands, they took it for granted that while he was at their head no such evil could possibly happen to them, and therefore were determined to immediately proclaim him king and rid themselves at once of Herod and the Romans.
Worldly wisdom would have said, "Declare yourself king; yield to the desires of the people; this will be the easiest way of converting them." Not yet understood was that Jesus must first deal with the problem of sin. Jesus must die for the sins of the world. There is no other remedy. Hebrews 10:1-18.

16 And when even was now come, his disciples went down unto the sea,
17 And entered into a ship, and went over the sea toward Capernaum. And it was now dark, and Jesus was not come to them.

The crowd was dispersed for the evening. Jesus was up on the mountain praying. Jesus' disciples set out by boat to travel in a westerly direction around the northern end of the the Sea of Galilee.

18 And the sea arose by reason of a great wind that blew.

[The sea arose] Not an unusual event. The sea of Galilee is located in the Jordan river valley and the mountains on either side funnel wind down the valley.

19 So when they had rowed about five and twenty or thirty furlongs, they see Jesus walking on the sea, and drawing nigh unto the ship: and they were afraid.

[Five and twenty or thirty furlongs] Between three and four miles. The Sea of Tiberias, on which they now were, was, according to Josephas, forty furlongs, or about 5 miles in breadth, and one hundred forty furlongs, or eighteen miles in length.

[They see Jesus walking on the sea] No problem for the God of the universe, who created the entire earth and all that is upon it, to require a few molecules of water to cling more tightly together and support him.
Consider this. Jesus could have flown, or simply appeared beside them in the boat if he wished. He chose to walk to them. Perhaps it was to come into their awareness more gradually and reduce the startle factor.

20 But he saith unto them, It is I; be not afraid.

Nevertheless, they were frightened until reassured by his voice.

21 Then they willingly received him into the ship: and immediately the ship was at the land whither they went.

Now, since they had just seen Jesus perform one miracle, another would not be so upsetting to them.

22 The day following, when the people which stood on the other side of the sea saw that there was none other boat there, save that one whereinto his disciples were entered, and that Jesus went not with his disciples into the boat, but that his disciples were gone away alone;
23 (Howbeit there came other boats from Tiberias nigh unto the place where they did eat bread, after that the Lord had given thanks:)
24 When the people therefore saw that Jesus was not there, neither his disciples, they also took shipping, and came to Capernaum, seeking for Jesus.

The following day people gathered again, including some who had newly arrived by boat. It became known that the the disciples had left for Capernaum. Jesus was not present either. There was no boat waiting to take Jesus away by water so the crowd determined that he would not be returning to that place on that day. The crowd set out for Capernaum.

25 And when they had found him on the other side of the sea, they said unto him, Rabbi, when camest thou hither?

[When camest thou hither?] Please solve this mystery for us. We know that you were not with the disciples when they put out from shore. No one saw you enter into another boat. How did you get here so quickly? Another miracle perhaps?

26 Jesus answered them and said, Verily, verily, I say unto you, Ye seek me, not because ye saw the miracles, but because ye did eat of the loaves, and were filled.

[Ye seek me, not because ye saw the miracles] Though the miracle of the loaves was one of the most astonishing that ever was wrought upon the earth; and this people had, by the testimony of their senses, the most convincing proof of it's reality, yet they little regarded the hand of God which was in it. Their attention was captured by the demands of their physical appetites.

27 Labour not for the meat which perisheth, but for that meat which endureth unto everlasting life, which the Son of man shall give unto you: for him hath God the Father sealed.

[Labor not for the meat which perisheth] Our Lord wills that every person be active and diligent in the service in which providence has placed him, but it is his will also that employment and all the concerns of life be subservient to the interest of his soul.

[But for the meat which endureth] Everything that can be posessed, except the salvation of God, is a perishing thing; this is it's essential character. But when the earth and it's produce are burned up, this bread of Christ, his grace and salvation, will remain eternally. This is the portion after which an immortal soul should seek.

[His hath God the Father sealed. By this expression our Lord points out the commission which, as the Messiah, he received from the Father, to be prophet and priest to an ignorant and sinful world.

28 Then said they unto him, What shall we do, that we might work the works of God?

[Work the works of God?] That is, Divine works, or such as God can approve.

29 Jesus answered and said unto them, This is the work of God, that ye believe on him whom he hath sent.

[This is the work of God] There is nothing in which you can be employed that is more acceptable to God than in yielding to the evidence set before you and acknowledging me as your Messiah and the savior of the lost world.