German theologian Rudolf Bultmann, in his famous and still widely cited commentary on John, wrote many decades ago:
The thesis has been represented, occasionally even in very early times but strongly from the beginning of this century, that the original order of the text [of John] has been disturbed, through an interchange of leaves or by some other means. …it must be presumed that the present order of our Gospel is not derived from the author. …It is not enough to reckon with a simple exchange of the pages of a loose codex, for the sections that appear to demand a change of position are of unequal length. The assumption lies closest to hand that the Gospel of John was edited from the author’s literary remains on the basis of separate manuscript pages, left without order. In any case, the present form of our Gospel is due to the work of a redactor. (pp. 11–12)
Bulfmann’s observations on the incongruities of the Gospel have been made and expanded on by many biblical scholars since then. Some agree that the Gospel seems to be out of sequence, as though an early manuscript were dropped and the pages put back in the wrong order. Others have proposed complicated source theories or stages of redaction, whether by the same author or an authorial community. Still others have simply ignored the problem altogether.

Regardless of which (if any) of these hypotheses is correct, the passages in John that have prompted this debate are worth having a look at.
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The Best Evidence for a Redactor: John’s Ending 📜
For any book of the Bible, but especially the New Testament, there are many conservative scholars whose audience is primarily devotional or pastoral and would prefer to understand the scriptures as discrete, synchronic works—each written by the person whose name appears in the title if at all possible, although that ship has long sailed for the most part.

As John Ashton notes, the lack of manuscript evidence is often cited by scholars in order to dismiss proposals for redaction and interpolation of texts. Chapter 21 of John is so clearly a secondary addition to the book, however, that this objection cannot be sustained. https://www.wolfson.ox.ac.uk/content/1140-dr-john-ashton
Once this rampart has been breached the enemy is within the gate: there can be no further defence of integral unity as a matter of principle, and the familiar argument that there is no manuscript evidence, either here or elsewhere, of editorial insertions or modifications loses all its force. (p. 42)
Some of the best reasons for considering John 21 (the “Johannine Appendix”) to be a later addition are the following:

• The story appears to end with a “resounding conclusion” in 20:30–31:
  Now Jesus did many other signs in the presence of his disciples, which are not written in this book. But these are written so that you may come to believe that Jesus is the Christ, the Son of God, and that through believing you may have life in his name.
  More:
• Chapter 21 makes the unnamed “Beloved Disciple” out to be the author of the book (21:24). This is not stated or suggested at any previous point. At the same time, the narrator takes pains to dispel rumours that the Beloved Disciple (whoever he was) would not die. As Bultmann puts it, “the fiction that the author himself puts himself forward here as identical with the Beloved Disciple, and at the same time wishes to attest his own death [v. 23] is quite unbelievable” (quoted in Ashton, 43).
• The style of the Johannine Appendix and nature of the miraculous catch of fish are considered to be quite different from the rest of John.
• The chapter is hard to understand from a narrative point of view. In chapter 20, Jesus appears to the disciples in a locked room, commissions them, and bestows the Holy Spirit upon them. And then in chapter 21, they go back to their old jobs as Galilean fishermen—which, unlike the Synoptics, is not even hinted at in John when the disciples are first called.
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  Geographical Aporias 📜
  Scholars often refer to the discontinuities in John as “aporias”, or paradoxes that cannot be resolved within the narrative. Some of these are geographical in nature. Jesus’ movements throughout the Gospel are frequently described in detail. Jesus went here, and the next day he went here, and then a few days later he went somewhere else, and so on. The author clearly intends to portray a coherent and meaningful sequence of destinations around Palestine where Jesus preaches and performs miracles. If you pay close attention, however, the geography of Jesus’ travels is often confusing, if not downright contradictory.
  John 6.1: One small step for a man…
  In John 5, Jesus is in Jerusalem for a festival. From verse 14 onward, Jesus is in the temple giving a sermon. And then, suddenly, in the very next verse (6.1), Jesus goes “to the other side of the Sea of Galilee”, implying he had been by the lakeside instead of in faraway Jerusalem. For this reason, Bultmann and others have suspected that chapter 6 originally followed 4, with chapter 5 misplaced in between. Other scholars see this as an indication of later editing or revision.

John 6.3, 15: Jesus and the mountain(s)

In John 6:3, Jesus goes up a mountain with his disciples and performs the miracle of the loaves and fishes. When the exuberant crowd decides to make Jesus king, he again withdraws to the mountain. The story seems to be missing something, since no departure from the mountain is mentioned in the meantime. https://www.biblegateway.com/passage/?search=john+6%3A3-15&version=NRSV

John 6.59: Synagogue scene change

After the miracle of the loaves and fishes, Jesus goes across the sea. The crowd follows him there, and when they find him at the sea, he gives a sermon. At the end of the sermon, we are told that Jesus has been speaking in a synagogue, though none was previously mentioned.

John 7.1: Judea or Galilee?

Another minor discontinuity takes place in John 7.1, which suggests that Jesus has left Judea and gone to Galilee. However, he was already in Galilee in the preceding chapter. Bultmann proposed that ch. 7 originally followed ch. 5, in which Jesus is is in Judea; and that both followed chs. 4 and 6, in which Jesus is in Galilee.

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Chronological Aporias 📜
Similarly, the timing of events in John is often confusing, despite (or perhaps because of) the frequent use of time markers.

John 2.1: How many days?

John’s story begins with John the Baptist at Bethany beyond the Jordan being questioned by priests and Levites. “The next day,” John sees Jesus (1.24). “The next day” again, two of John’s disciples leave him to follow Jesus (1.35–42). “The next day” after that, Jesus decides to go to Galilee (1.43). Then, “on the third day”, a wedding takes place in Cana of Galilee (2.1). (Read the entire passage here.) If the third day of the narrative is meant, we are already on the fifth day. If the third day of Jesus’ trip to Galilee meant, the geography is problematic; that’s a journey of about 110 kilometres (70 miles), which cannot realistically be accomplished in three days (see Brodie, p. 164). If Jesus and his disciples are travelling by donkey, one can expect a speed of about 10–12 miles per day.
It is easy to see why many take the passage to have been composed in stages and possibly out of order

John 10.22: Where does the time go?

In 7.10, Jesus goes in secret to Judea for the festival of Booths. Jesus spends the festival preaching, as well as healing a man blind from birth, with no change in time or place suggested. Yet suddenly in 10.22, it is two months later, and the feast of the Dedication is taking place
We may also note that the transition from Jesus’ arguments with the Pharisees at the end of ch. 9 to his discourse on the Good Shepherd in 10.1–18 is very abrupt (https://www.biblegateway.com/passage/?search=John+9%3A35-10%3A18&version=NRSV), with no clear logical connection. This section is followed by a controversy about Jesus being demon-possessed in 10.19–21, which contextually belongs with the healing of the blind man at the beginning of ch. 9. (Similarly, all three Synoptics use Jesus’ healing of the blind/mute man to introduce a controversy on demon-possession.)
Furthermore, Ashton notes that chapters 9 and 10 presuppose different historical situations for the Johannine community. Ch. 9 implies that the Christians are still part of the Jewish synagogue but are in danger of being expelled for professing their beliefs in Christ. In chapter 10, and in the Good Shepherd discourse particularly, the Christian community is portrayed as a self-sufficient group that is threatened by outsiders. (Ashton 2007, 48–49)
John 11.2: There’s something about Mary

In chapter 11, we learn that Lazarus of Bethany, brother of Mary and Martha, has fallen ill. The narrator explains that this is the same Mary “who anointed the Lord with perfume and wiped his feet with her hair.” The odd thing about this explanation is that Mary’s anointing of Jesus hasn’t happened yet at this point in the story. (It takes place in chapter 12.)

John 12.44: Hiding in plain sight

John 12 has Jesus preaching to the crowd (12.27–36), and then leaving and hiding from them because of their unbelief. However, his public preaching inexplicably resumes in v. 44.

John 14.31: The Sermon in the Alley

In chapter 12, Jesus pays his final visit to Jerusalem and spends the Last Supper with his disciples. After spending two chapters preaching the Farewell Discourse to them, Jesus apparently decides to leave, saying, “Rise, let us be on our way” (14.31). He then continues his speech (15.1) for another three chapters as if nothing had changed until he and his disciples actually leave in 18.1. Some scholars think the Farewell Discourse originally ended at 14.31, and that chs. 15 and 16 are an addition reflecting a later situation in the Johannine community (Ashton 2007, 137).
John 13:36, 16:5: Quo vadis?

In John 16:5, Jesus declares, “But now I am going to him who sent me; yet none of you asks me, ‘Where are you going?’” However, Simon Peter just recently asked in 13:36, “Lord, where are you going?” Paul N. Anderson asks,

Was the text disordered and reordered wrongly, was Jesus not paying attention, or does this perplexity reflect a diachronic relationship between the material in John 13 and 16, alleviated by seeing one passage or the other as part of another source or edition? (2009, p. 248)
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Parallel texts between gJohn and Synoptics: