There is no doubt in the writing of the author of John as to whether Jesus loved that disciple. Is this a physical as well as spiritual love? There is nothing in John to either verify or deny this speculation. However, in the Gnostic scriptures, also known as the Dead Sea scrolls, there is some mention of Mary Magdalene being Jesus’ favorite.
The Gnostic Scriptures: One fascinating verse has Peter resentfully asking Jesus why he loves Mary Magdalene, a mere woman, best of all his followers. Jesus’ tart reply is Peter might want to try emulating Mary more, rather than whining so. Peter was always jealous of Mary, according to the Gnostic scriptures.
Unfortunately Peter got the “last laugh” — he and Paul are historically credited with the creation of the fledgling christian church — rather than Mary — even though Jesus was supposed to have taught Mary more of his mysteries than any other of his followers. Sadly, even though she was quite willing to share her teachings, Peter apparently never forgave her for her closer relationship to Jesus.
This — a “mere woman” being Jesus’ favorite — might not be such a radical thought to the Gnostics, since they believed Jesus was pure spirit, and there is no carnality in spirit. However, the later Apostles or their followers might find the notion, even if true, of a female being Jesus’ favorite disturbing — it brings up unwanted allegations of possible sexuality.
Apostles & sex?! Many, if not all, of the Apostles were married. Examples: Matthew 8:14 and 1 Corinthians 9:5.
This would be doubly annoying if it was indeed true — that God’s “Chosen Pure One” might enjoy sex would be to sully the pristine public relations image of Jesus that was being presented to the world at that time. Carnality is not part of the Christian concept of Christ. Better to simply remove any mention of such a religiously embarrassing thing.
It would be symmetrical, however, for Jesus to have a female companion. Was not Jesus’ Father supposed to have had his Sophia, mentioned in the Old Testament? Proverbs mentions “Sophia”; Philo Judaeus used “Logos.” This doesn’t mean the female concept is lost, only that Philo wished Jesus to be God’s “companion.” The divine Logos (or Jesus) may have wanted some wise counsel while he was flesh. How appropriate to emulate his Father, and to pick a wise woman to counsel him.
Sophia means, roughly, wisdom in female form. Yahweh and Sophia were male and female, and traditionally creation came about by their union. Philo Judaeus was an early, emphatically non-Gnostic writer. Logos roughly means wisdom in the male linguistic form. P.J. probably wanted Logos to be male so Yahweh and Wisdom were respectively exemplified by God and Jesus, his son. Including the sexless Holy Spirit in this group formed the Trinity — no females need apply!
Finally, in John 21:21, the scene where Jesus has risen from the dead and is telling his apostles good-bye and good luck, Peter asks “Lord, what will happen to him?” referring to the disciple Jesus loved.
Why should Peter worry more about this person than any of the other apostles? It would make more sense if this person were a female, and now with Jesus’ death legally without a protector or guardian.
Furthermore, Jesus tells this person to follow him, away from all the other apostles, for some small, unspecified amount of time. As far as I know, privacy is a requirement for love-making in almost all cultures, Judaism included. My fanciful thought was perhaps Jesus wished one final night in the flesh with the disciple he loved.