When evening came, the boat was in the middle of the sea, and Jesus was alone on land.
This passage of story we had Mat 14:22, etc., only what was there related concerning Peter, is omitted here. Here we have, I. The dispersing of the assembly; Christ constrained his disciples to go before by ship to Bethsaida, intending to follow them, as they supposed, by land. The people were loth to scatter, so that it cost him some time and pains to send them away.
Commenting on Mark 6:45-56
And he saw them toiling in rowing,.... He saw them either with his bodily eyes from the mountain on which he was; or he perceived in his Spirit, he knew, by virtue of his omniscience as God, what distress his disciples were in; being tossed about with the waves of the sea, and were labouring with all their might and main against the wind: and...
The ship was in the midst of the sea - See all the parts of this wonderful transaction considered, on Mat 14:22-33 (note).