John Gill Commentary John 6:17

"and they entered into a boat, and were going over the sea unto Capernaum. And it was now dark, and Jesus had not yet come to them." — John 6:17 (ASV)

And entered into a ship
In which they came, and was waiting for them; or into another:

and went over the sea towards Capernaum ;
steered their course from Bethsaida, where they took shipping over the sea of Galilee; at least over one part of it, a creek or bay of it, as they intended, towards the city of Capernaum, which lay over against Bethsaida:

and it was now dark ;
quite night, which made their voyage more uncomfortable, especially as it afterwards was tempestuous: but the worst of all was,

and Jesus was not come to them ;
as they expected, and therefore were obliged to set sail and go without him.