Jesus told the disciples that up to this time he had spoken to them in proverbs (G3942). That is, he spoke to them with illustrations like: behold the lilies of the field or the birds of the air, or through the example of washing their feet etc. Nevertheless, the time was coming when he would speak to them clearly, and they would understand (John 16:25). He spoke of that day (John 16:23), when he would be in them (John 14:17; cp. Colossians 1:27), whereby his Spirit would be in union with their spirits (2Peter 1:4), and they would be able to understand spiritual matters (1Corinthians 2:11-13). However, at present they could not understand Jesus’ plainness of speech, because he spoke of things, which could be understood only by knowing other spiritual things and comparing them together (1Corinthians 2:14).
Yet, such intimate knowledge wouldn’t be understood until that day, that is, when they would have the Spirit of Christ in them (cp. John 14:17; Colossians 1:27), and in that day they would pray to the Father in Jesus’ name. In other words, because the believer’s spirit is united with Christ’s Spirit, which is ONE with the Father, the believer has access to God. No mediator would be needed. Up to this time they had needed a priest to pray for them, but coming in Jesus’ name, that is coming to the Father, because they love Jesus, and believe he had come forth from beside the Father, they, the believers, had direct access to the Father. Such access is possible only because of their union with Jesus’ Spirit. Therefore, a mediator is no longer necessary, because the Father loves us and doesn’t need anyone to remind him of who his children are (John 16:26-27).
Then Jesus said again: “I came forth from beside the Father and came into the world. Now, I am leaving the world and returning to the Father’s side” (John 16:28; paraphrased), and Jesus’ disciples responded with (paraphrased): “Now, you are speaking with us clearly and without proverbs (cp. John 16:29, cp verse-25). Now we know that you know all things, and no one needs to ask you to pray to the Father for them. By this we know we know that you came out and apart from God” (John 16:29-30). Thus, their own statement revealed their ignorance and inability to understand what Jesus told them clearly. He was speaking of his divinity that he came forth from beside God (cp. John 1:1), but they understood him to say he came out apart from God, much like an angel might be sent out from God’s presence, but once sent out was no longer in God’s presence. Jesus, on the other hand, came forth from beside God, and was, in fact, God (John 1:1). Therefore, the presence of God continued to be wherever Jesus was. Such a concept was similar to the idea that by taking the Tabernacle from place to place, one brought God’s presence from place to place.
Speaking ironically, Jesus says: “Now, you believe?” In other words, you actually think that you understand these things before the time I’ve indicated? You, think you believe according to knowledge, now, before your spirit is united with mine? Such faith is baseless and would be unable to persist. In fact, in this very night they would flee from Jesus’ presence, leaving him alone with his enemies. Yet, he would not be alone, because he had not come as they concluded: out and apart from God, but he came forth from beside God and was even at this time present with God, his Father (John 16:31-32, cp. John 1:1, 18).
Nevertheless, far from blaming them for their inconsistency, Jesus said he had spoken these things to them that they might have peace. After Jesus returns to the Father and their spirits are united with the Spirit of Christ, the Spirit will bring all things to their memory that Jesus had spoken to them. These words would come to mind, when the tribulation begins, which will inevitably be theirs in the world. However, they can be assured of peace in it all, because of the fact he would make his abode in them. They would have the joy of knowing all things are occurring in the very presence of God, and therein would be their peace (John 16:33).