John writes his gospel with the aim of showing that “Jesus is the Christ, the Son of God” (20:31). He does this in a number of ways:
1. By making some very direct theological statements concerning Jesus; the most profound is that he makes Jesus equal with God (John 1:1-18; cf. 5:18).
2. By telling us about some of the signs that Jesus did. By this He proved that He had the ability to do things that only God could do. Nobody spontaneously makes wine out of water (2:1-11); nobody feeds 5000 people with only 5 loaves and two fishes (6:1-15). Nobody suspends the laws of nature by walking on water (6:16-21). Nobody raises people that have been dead for 4 days, to life (11:1-44)
3. By recording some of the profound conversations that Jesus had with various people (i.e. with Nicodemus here, and with the Samaritan woman at the well in Chapter 4). In these conversations Jesus reveals what He calls ‘heavenly things’ (3:12). He reveals the way into the kingdom of God (3:3, 5), a kingdom infinitely bigger than geographical Israel. In these conversations He invites people to believe in Him (3:16, 18) that they may enter into eternal life. During the course of these conversations it becomes very clear how ignorant Jews (Nicodemus) and gentiles (The Samaritan woman) were about these things. Many in our world are just like that. People’s understanding of God and of Christ and of the work of the Holy Spirit is too small. Our understanding of the serious effects of the fall is stunted and the nature of our sin is underrated. Most people believe that they have the capacity to work out their salvation through good works. Most people believe that they are going to heaven.
Our text focuses on the conversation of a Pharisee named Nicodemus.
He comes to Jesus by night, perhaps for fear of being seen. The preceding context is important here. In John 2:23 we read that Jesus performed more of His miraculous signs in Jerusalem during the Passover feast. They are not recorded - see the comment in Jn. 20:30. The result is important to note: "many believed in his name when they saw the signs that he was doing.”
Nicodemus was one of these many who saw these miraculous signs being done. He says to Jesus, "Rabbi, we know that you are a teacher come from God, for no one can do these signs that you do unless God is with him." And we, in our own minds may be thinking, "this man is a convert. He is one Pharisee who has come to believe in Jesus, because he saw the signs.” But, not so! John 2:24-25 says,  “But Jesus on his part did not entrust himself to them, for He knew all people and needed no one to bear witness about man, for he himself knew what was in a man."
Now what did Jesus know about these so-called believers, like Nicodemus that caused Him to not entrust Himself to them? The answer is given in our text. Jesus knew that Nicodemus, the religious man and leader that he was, was not born again. Jesus knew what was in Nicodemus. The problem with religious men like Nicodemus is that he is not born again. He does not really know God. He does not know what this kingdom of God is all about.
And, so without much further ado, Jesus tells him, “Truly, truly I say to you, unless one is born again he cannot see the kingdom of God.” (3:3)
Now Nicodemus is really confused. Jesus is speaking here of the necessity of a birth. The only birth he knows of is the birth which a woman gives to a baby. So what is this ‘born again’? Bewildered he asks a sort of logical question, “How can a man be born (again) when he is old? Can he enter a second time into his mother’s womb and be born?” (3:4). So Jesus repeats himself, “Truly, truly, I say to you, unless one is born of water and the Spirit, he cannot enter the kingdom of God”. He is repeating the same thing, but He adds a phrase, ‘born of water and the Spirit’.
The subject is still the regenerating work of the Holy Spirit, but what is the meaning of the water? There are a number of views here. We will not elaborate on them all. Both, water and the Spirit often refer symbolically in the OT to spiritual renewal and cleansing. That’s what John came to do (see John 1). He called people to spiritual renewal and cleansing through baptism in water. The Spirit baptism he left to the Messiah (1:33), but both pointed to the same thing- a renewal, a cleansing, a washing from the horrible effects of sin.
And now we must also refer to Ezekiel’s prophecy, which is an allusion to the new covenant. Here God says through Ezekiel, 24 I will take you from the nations and gather you from all the countries and bring you into your own land. 25 I will sprinkle clean water on you, and you shall be clean from all your uncleannesses, and from all your idols I will cleanse you. 26 And I will give you a new heart, and a new spirit I will put within you. And I will remove the heart of stone from your flesh and give you a heart of flesh. 27 And I will put my Spirit within you, and cause you to walk in my statutes and be careful to obey my rules. (Ezek. 36:24–27)
With the context of John 1 (John’s baptism) in mind, and Ezekiel’s prophecy pointing to the new covenant (the Spirit baptism associated with water), we can be fairly sure that this is what Jesus had in mind. Without the spiritual washing of the soul (symbolised in water baptism), accomplished by the regenerating work of the Holy Spirit, no one can enter God’s kingdom. And so Jesus explains this further to Nicodemus: “Nicodemus, in order to enter the kingdom of God you must not only be born once. You must be born twice. Your first birth is flesh - and it gives you a human nature. The second birth – gives you a spiritual nature.” In fact, it replaces that which was lost in the fall through sin (Genesis 3). So, "do not marvel that I said to you, You must be born again “(3:7). In order to see the kingdom of God (3:3), and to enter the kingdom of God (3:5), you must be born again.
The mystery of the new birth is now explained. “Nicodemus, the wind (the Spirit) blows where it wishes and you hear its sound, but you do not know where it comes from or where it goes. So it is with everyone born of the Spirit. It is a sovereign work of the Holy Spirit, in which you have no part – just like you have no part in your first birth” (3:8).
You do not initiate your new birth any more than you give birth to your own body. You do not initiate your spiritual birth any more than Lazarus initiated his resurrection. The resurrection of Lazarus to new life was owing to one thing: the word of Jesus Christ—“ Lazarus, come out!” [John 11: 43]. The word that makes people come alive, is the Word of Jesus, as it is applied by the Holy Spirit. When the Holy Spirit is upon the message there is an explosion of life. The Word and the Spirit give new life to dead hearts. When the gospel is preached and the Holy Spirit says, “Let there be life”, the eyes of the heart are opened, and a person is born again! May it be so today!
Nicodemus is now utterly confused, “How can these things be?”(3:9).Jesus says to him, “Nicodemus, you are a spiritual teacher in Israel , and yet you do not understand these things?” (3:10).
What we learn here in John 3:3-10 is Jesus’ view of “what is in man”. The people that were marveling at His signs, and even this religious teacher of the Pharisees, Nicodemus, have no true perspective of those Scriptures which they claim to search. They have no true idea who God is and what the kingdom of God is. They have no understanding of the person and the nature of the long prophesied Messiah, who is right here before their very eyes. If the truth be told … they are dead.
Jesus however does not leave Nicodemus without an answer, “You must be born again!”
What is the nature of a man who is not born again?
He is mere flesh. Flesh in John 3:6 refers to human nature out of touch with God. It results in all sorts of problems, described in Galatians 5:19-21: “The works of the flesh) are evident: sexual immorality, impurity, sensuality, idolatry, sorcery, enmity, strife, jealousy, fits of anger, rivalries, dissensions, divisions, envy, drunkenness, orgies and things like these. I warn you, as I warned you before , that those who do such things will not inherit the kingdom of God."
“Flesh gives birth to flesh.”
Who is mere flesh?
All people, since all are born in this way. All people, everywhere, by nature, are cut off from God. "We have all sinned and fallen short of the glory of God. (Rom 3:23). Apart from being born again by the Holy Spirit, all of humanity is, from God’s perspective, totally depraved. There is no sufficient moral good in any of us to make us acceptable before this holy God. The flesh may have the capacity to compose beautiful music, and send spaceships to Mars, design and build and invent wonderful things - but all these achievements are of no moral value in God’s sight. Wherever man does not humbly rely on God for power, the product of his brain is an idol (Rom. 14:23- Whatever does not proceed from faith – even my preaching to you - is sin).
Since religion is such a common substitute for the real thing , i.e the new birth, each of us ought to examine ourselves to see if we are truly born of God (2 Cor. 13:5). I say this with trembling… but many, many people in our churches are utterly minimalistic when it comes to portraying the born again life, in terms of loving God, loving one another… I fear for religious people in our churches.
These words of Jesus must have rocked Nicodemus’ heart and soul. Jesus’ words must have pierced his hearts and they must have humbled this ruler of the Jews “… Nicodemus, you are a spiritual teacher in Israel, and yet you do not understand these things? Truly, truly I say to you (3rd time in this conversation), we speak of what we know, and bear witness to what we have seen .” Jesus is including John the Baptist or the disciples in the ‘we’ (cf. John 1:14,15) , but you (Plural – meaning the Jewish people whom Nicodemus represented) if I have told you earthly things and you do not believe, how can you believe if I tell you heavenly things?”
Jesus had employed earthly metaphors such as birth (for the new birth) and the wind (for the Holy Spirit), and yet Nicodemus, and those whom he represented refused to believe (3:12). How will they possibly understand and accept a still more direct language, like “I AM YOUR CREATOR- THEREFORE COME TO ME AND I WILL HEAL YOU FROM YOUR BLINDNESS, DEAFNESS AND HARDNESS OF HEART?”
Jesus knew what He is talking about, for His own origins were from heaven. He descended from heaven. He is, right now, the ascended Christ (3:13).
Which brings me to my final words. Jesus is preparing Nicodemus for a work of grace : "In fact, Nicodemus, I am telling you now that I am here to do a great work for all who will believe."
The OT under Moses has left a great illustration for us in Numbers 21:9 ff. When Moses used the image of an upraised snake in the desert, to be looked at, and so to save from death those that were bitten by snakes, Jesus saw Himself in this picture as the One lifted up on a cross to save all those who would look to Him and believe in Him.
Jesus, lifted up on the cross for us to behold is a far greater saving achievement than Moses.People healed from their snakebites will die again. People who look to Jesus for the healing of sin's lethal effects will live for eternity.
All this leads us to that great statement in John 3:16, perhaps the most quoted verse in the Bible. I will have to leave this for next time.
Dear friends, Christ has been clearly portrayed before you. Who is He to you?And those of you, who are still half committed and religious, how will you escape the coming wrath if you continue to ignore this Christ?
What will you do on the day of His coming?
This is an invitation to believe in Jesus – His person and work! Embrace Him, love Him with all your heart soul mind and strength.
 Note: this is very similar to the story of the rich young ruler in Mark 10
 cf. Num. 19:17–19; Isa. 4:4; 32:15; 44:3; 55:1; Joel 2:28–29; Zech. 13:1
 See Isaiah 6:1-7- Isaiah overcome with the holiness of God