I've been through the Gospel of John at least three times with people, once in Greek, and each time I find something new. Each time I see that the words of the gospel change the hearts of all who hear it. I have tried even to go through the Gospel of John with people online, taking one verse at a time, in the hopes that the words of our Lord will melt the hearts and open the minds of the ones hearing or reading. One time, I had a lengthy discussion with a close friend about the first few verses of John, until I realized that he just didn't believe God existed. His was the argument from evil: the world was a bad place and so how can there be a good God who created such a bad place? I tried different arguments of reasoning, but they all fell on deaf ears. I decided the take a different approach and leap right to the end of the Gospel of John: to where Thomas doubts. That, I surmised, was the place where my friend was, and so maybe if we tackled that section first, we may make some headway. We didn't get far. Not only did my friend not believe in God but he didn't even believe that the Bible had any meaning. It was nonsense to him, and so we couldn't even use the text to continue.
Looking at the text itself, we can see how important the Word of God is for those who believe and will come to believe. We cannot argue one into the kingdom of God with well-spoken logic. Instead, we open the text before the one in question, and the Holy Spirit illuminates the truth for him, opens the eyes of his heart, and breathes life into his dead soul. The passage of text in question (John 20:24-end) says that Thomas, one of the twelve, one of the Apostles, someone who has followed Jesus from the beginning of his ministry, was not there to witness the risen Christ. None of us who live today were there, either, to witness the risen Christ, and so we are very much in the same boat. I wasn't there, nor was my friend. Thomas wasn't there (the first time), and when the other disciples said to him that they had seen the risen Lord, he doubted and told that he would not believe in Jesus until he had physically touched him, including putting his fingers in the wounds. He was quite confident that his doubts were justified.
Eight days later, Jesus showed up again, appearing suddenly in a shut room among them, offering peace. Christ did not wait for someone to tell him that Thomas is here! and he wasn't here the week before, and guess what, Jesus! Thomas won't believe in you until he, etc. etc. Jesus does not wait for someone to tell him what he already knows, he goes to Thomas directly and tells him to put his fingers in his wounds. "Do not be unbelieving but believing," he tells him. Thomas now believes and says, "My Lord and my God!" what an amazing and emotional scene. Jesus then gives us a message directly: "Blessed are they who did not see, and yet believed." That's us, believers who never got to put their fingers into his wounds, and yet we believe whole-heartedly. And yet...
And yet there are they who have not seen and still do not believe. We know about them, we see them every day, and we know that their minds and hearts are closed to the gospel. We pray for God to open their eyes, so they can finally be seeing the truth that we all see. And then, worse, are those who do see Jesus, who can actually see the work of Jesus Christ in their lives. As their creator and sustainer they owe their very lives to him, and yet, they do not believe. Miracles have happened to them. Evidence for God has come pouring down upon their heads. And still they do not believe. The Bible has been opened to them, the words have been read to them, and still their hearts are dead lumps of coal. These are the ones whom we need to pray for. How do we get through to them, when they have seen and heard, and yet their hearts refuse to see or hear?
John answers this question right afterward. He writes that many miracles and signs Jesus performed are not written in his gospel, but what is written here has been written "so that you may believe that Jesus is the Christ, the Son of God; and that believing you may have life in His name." These verses are not at the very end of the book but at the end of the penultimate chapter, because they are supposed to be attached to the Thomas narrative. Many need proof to believe, but many do not believe even with proof. Finally, many believe without proof, and these are the true believers, because the Holy Spirit opened the eyes of their hearts. We live in a fallen world, where the proof of God's existence exudes from every pore of nature, and yet the eyes of most of the world is veiled. No amount of persuasion can soften the hearts of stone, but anything is possible with God, and if we believers--by faith--pray for the unbelieving world and work to get the Word of God into their hands, we can watch God work his wonders firsthand.