It was now dark (skotia ēdē egegonei). Past perfect active of ginomai. While they were going, “darkness had already come.”
And Jesus had not yet come to them (kai ouk elēluthei pros autous ho Iēsous). Another past perfect active of erchomai with negative oupō. Darkness had come, but Jesus had not come, while they were going over the sea. The tenses in these verses are very graphic.