Jesus' conversation with Nicodemus in John chapter 3 can seem awkward at three points.
Throughout the gospel narrative, Jesus' words occasionally can seem to jump unexpectedly from one topic to another. Whenever this appears to be the case, we can be certain that the reason is not that Jesus was following flights of fancy where mental organization would better suit, but that our understanding of the subtleties of the passage is inadequate. For a clear understanding of Jesus' conversation with Nicodemus, the context to consider is more than just the immediately surrounding passages. In this case, the circumstances under which it occurred also bear strongly on the meaning. Nicodemus was a Pharisee and a ruler of the Jews. He had both religious and civic leadership. So we must take into account all passages that give us information about the relationship between Jesus and the Pharisees and rulers.
For instance, in Matthew 9:11, we find the Pharisees upset at Jesus for consorting with people they looked down on. In verse 34, they considered Jesus' power to cast out demons to come from the devil himself. They were always looking for some way to catch Jesus in a contradiction or dilemma, or trying to get him to say something that would make him look bad, as in the case of divorce in Mark 10. By Matthew 12, the Pharisees were already plotting to kill him.
This is only a representative start, not a thorough investigation, but it will do for the purposes of this article. For any member of the Pharisaical sect to have a friendly conversation with Jesus would be considered consorting with the enemy, with public enemy number one, in their eyes. To be caught doing so would have meant that Nicodemus would lose a great deal of his influence and status.
But he came anyway. Notice in John 3:2 that he came by night. This was done to maintain secrecy. That he was successful in keeping his visit secret is evident from John 7, where he tries weakly to protect Jesus from an unfair arrest, and is asked by his fellow Pharisees, "What, are you from Galilee, too, now? Look into the prophecies and you'll find that the Christ is not supposed to be a Galilean" (my paraphrase). They seem surprised at him, indicating that they had no inkling he had been converted.
Keeping Nicodemus' circumstances in mind, ponder the reason for his opening confession, "Rabbi, we know that You have come from God as a teacher; for no one can do these signs unless God is with him." What is behind his words, between the lines? He's saying, "OK, look. You and I both know how we Pharisees have given you down the road for challenging our piety and authority. But just between you and me and the garden wall, we know you are from God. We know God is the source of your words and your power, whatever we might accuse you of in public." This is an astonishing confession. You can almost hear him gulping, see him shifting his feet, feel him turning a little red, as he says it. It very nearly amounts to an admission that Jesus is the Messiah; for who has truly "come from God" but "He who descended from heaven," as Jesus points out in verse 13. A Pharisee would not lightly use such words as "you have come from God" and "God is with you" of any Rabbi. His confession raises the question, if they suspect Jesus' true identity, why is Nicodemus the only man there that night? Why are the rest not lined up on the sidewalk behind him, waiting their turns?
Now consider Jesus' response, "Unless one is born again, he cannot see the kingdom of God." Taking the common interpretation of these words, that is, "You, Nicodemus, need to be born again," Jesus seems to be completely ignoring Nicodemus' striking circumstances and remarkable confession altogether; if so, He is ignoring the proverbial elephant in the room. For all the unexpected things that Jesus said and did during His earthly ministry, that tack would be unlike Him. But there is a way to view His response that allows for and clarifies the entire context.
If behind Nicodemus' confession lies the understanding that there is something notably odd about the fact that he has to go surreptitiously to avoid detection by his religious cohorts, when they suspect as strongly as he does that Jesus is the Messiah, then the intent of Jesus' words would be, "Nicodemus, they do not come because they have not been born into the kingdom of God." And that is as much as to imply, "But you have." This is not as surprising as it might at first seem, in light of the fact that the only other two references to this man show him to be a friend of Jesus. John 7:50, 19:39
But doesn't Jesus tell Nicodemus, in verses 11 and 12, that he doesn't yet believe? Maybe. But as far as I can discern, the words for "you" in those verses are in plural form. If so, then Jesus is there speaking of the Pharisees as a group, not of Nicodemus particularly. In any case, the Spirit must have been drawing Nicodemus already or he would not have risked so much in an attempt to give Jesus the inside scoop. If he did not yet understand the true nature of the kingdom of God, and therefore could not believe in it in the fullest sense, does that necesarily mean that he was not yet regenerated, or that he did not yet have saving faith in Christ Himself?
Spiritually, then, he was a newborn infant, in need of the most basic teaching. And that is exactly what Jesus then proceeds to give him. In verse 13, He openly declares His identity as the Eternal One sent down to earth from heaven. Then He reminds Nicodemus of the event recorded in Numbers 21, where Moses lifted a serpent on a bronze staff as a cure for a plague that God had sent among His people. This story was well known to all Jews; but very likely, no teacher had yet recognized it as a Messianic passage. Jesus uses that familiar reference point as a launch pad from which to lay out the gospel in the simplest and clearest of terms in verses 14-18: look and live.
It might seem from this that Nicodemus must not be born again yet, since Jesus takes the time to explain the gospel to him. But Christ and the apostles didn't portray the gospel as an invitation to the unbeliever, but as the means by which the Spirit creates faith in the hearts of the elect, and as the power of God unto salvation for those who do believe. Romans 1:16 An unbeliever cannot understand the gospel, so, though we preach it to all for the sake of those who will believe, it is of no use to explicate it for unbelievers. Jesus' patient explanation of the gospel to Nicodemus, then, is further evidence for, not against, the conclusion that he was already born again, if very newly.
In the end, Jesus circles back around to addressing the issue Nicodemus had initially raised. In verses 19-21 He gets very specific about why Nicodemus came to Him while the others remained at enmity: Jesus is the light that is come into the world; the other Pharisees were evildoers, and did not want their dark deeds exposed by the light; that Nicodemus came to the light shows that he was a practicer of the truth, whose deeds were wrought in God. That he came willingly is more than evident from the great risk he took to do so. Jesus' words in these three verses, then, further confirm that Nicodemus had already received regeneration; otherwise he would never have come to the light at all.
In that case, His words in verses 3-8 cannot be taken as directed at Nicodemus, instructing him to be born again. In the first place, it makes very little sense to think in terms of instructing someone to be born. But more to the point, taking that interpretation removes reasonable flow from the conversation at three points. It thereby muddies up the whole text. One plague that results is the isolation of the three sections from each other, theologically, resulting in a fragmented soteriology in which the relationships between regeneration, faith, and response are ill understood.
But by taking the interpretation that Jesus' purpose was to answer Nicodemus' perplexity over how his fellow Pharisees could see Him fulfilling one Messianic prophecy after another, and yet remain opposed to Him, clarity and flow are restored. We may then perceive the full picture that this passage provides of the nature of the kingdom of God as pertains to entering it. First, the Holy Spirit gives birth to a new spirit. Then the spiritual newborn sees, with the eye of faith, the Son of Man lifted up as the only cure for his sinful condition. He then responds, drawn to the Light of the world to receive the pure milk of the Word, as surely as an infant is drawn to its mother's breast. It's a beautiful, touching picture, and succeeds in reserving all due credit for salvation to God alone, in Christ alone, by grace alone, through faith alone, on the authority of God's Word alone.