The effect of Jesus’ words about Judas was confusion in the minds of the disciples because they could not imagine to which one of them Jesus was referring. Other Gospel accounts indicate that each was concerned in case Jesus was referring to him in particular. Peter, as we would expect, was not only confused; he was also curious to know which disciple Jesus had in mind. So he asked John, the disciple whom Jesus loved, to ask Jesus for more information.
This particular relationship that John had with Jesus was a very precious one. Here are five details about it.
First, there were degrees of intimacy between Jesus and his disciples. We know that of the twelve there was an inner group of three (Peter, James and John), and of the three there was one who was closer to Jesus than the other two (John).
Second, the fact that Jesus loved John in a special way was not a reason for jealousy in the other disciples. Indeed it is possible that it was them who first called John by this name (the disciple whom Jesus loved), once they noted how intimate the relationship was. There is no suggestion that any of them objected to this display of divine favour.
Third, recording this detail is not evidence of pride of John’s part when he, as the author of this Gospel, says that he had a special relationship with Jesus. Rather it is an expression of genuine wonder that he had been so favoured by Jesus.
Fourth, what reasons can be given for explaining this special relationship between Jesus and John? One possibility is that Jesus as a human had close friends. Another possibility is that Jesus and John were cousins; it can be argued from a comparison of John 19:25 and Mark 15:40 (the women at the cross) that Mary (Jesus’ mother) and Salome (John’s mother) were sisters. While these suggestions are valid, they do not explain the relationship. The only explanation is that it was a matter of divine choice.
Fifth, this divine privilege did not mean that John was not responsible for maintaining a right spiritual state in order to enjoy the relationship. In his case, as with the enjoyment of all spiritual blessings, there would have been confession of sin and faith in God’s promises. His response to Jesus here also points to other aspects: acceptance of Jesus’ sovereignty (Lord), approach marked by straightforwardness, acquiescence in serving another disciple (Peter), and anticipation of receiving an answer.