Now the birth of Jesus Christ was as follows: when His mother Mary had been betrothed to Joseph, before they came together she was found to be with child by the Holy Spirit. And Joseph her husband, being a righteous man and not wanting to disgrace her, planned to send her away secretly. (Matthew 1:18-19)
Point 1: God uses perplexities to prepare the heart for more satisfying revelation. It is good that we be confused before a revelation, because then the magnitude of the revelation becomes more complete and clear. This is what happened to Joseph as he pondered what to do with Mary. She had a visible pregnancy, so he could understand that, but he did not understand the divine aspect of the situation. He knew she was honorable, so he did not wan to make a spectacle of her but "put her away quietly." Joseph is in perplexity. He knows Mary is pregnant, but he does not understand the holy manner of the pregnancy. In other words, he does not believe. He has a faith issue. Joseph's decision to put Mary away secretly marks the beginning of Christ's sufferings. He is confused, but he has correct information. She is pregnant, but she is not an adulterer. All he needs is a revelation of the truth to give him the faith to do the right thing, which is to marry her. God waited to do this until Mary had been espoused to Joseph, so there would be no "wagging of tongues." He was a just man, so he was not going to call her out publicly. But he needed to do something, so he was intending to put her away secretly. The revelation from the angel gave him the peace and clarity to do the right thing.
Point 2: Before revelation, in our perplexity we are in a state of rejecting God. Even the elect reject Christ before understanding. The perplexity plus the fact that the Spirit hasn't manifested Christ yet to us equals rejection, just as Joseph was to do. It is good to be perplexed, even though we are in a state of rejecting Christ. As long as the garden of perplexity is honest, as long as we are being honest doubters, the revelation that comes afterward will be satisfying. Seek out the truth, no matter where it leads, and you will find it.
Point 3: The world will intentionally obfuscate the truth so that we cannot find it. The world wants you to stay in a perpetual state of perplexity, so that you will then be in a perpetual state of rejecting God. The world does this by giving us dishonest perplexity, by giving us false information to use. Always go to the Bible for the proper knowledge with which to wrestle. Here are some examples:
It is important that we always join "of the Holy Ghost" to the virgin birth. We must provide no opportunity to think blasphemous thoughts about Christ and the nature of his birth. This means knowing the Holy Ghost intimately. So many times I hear someone blasphemously say or write that the Holy Ghost "knocked up" Mary. Lately a college professor has gained attention by claiming that Mary did not "provide consent," implying that the Lord raped her. This is dishonest rhetoric that clouds the issue and keeps people in a perpetual state of rejecting Christ. Go to the Bible and see that it always mentions the Holy Spirit as instrumental in Mary's conception. Even Mary was perplexed at the angel's words in Luke 1, until the angel mentioned the Holy Spirit, and then Mary was satisfied. For comparison, see Zacharias in the same chapter who, even though Elizabeth's was not a virgin birth, was given all the necessary information from the angel, and yet he still doubted. The forced muting of his voice until the birth was the extra revelation he needed to believe.
Another example: Mary is not the mother of God. This is confusing theology. She is the mother of the human nature of Christ through her virginity. Christ is eternal, so when a denomination uses phrasing like "Mary, Mother of God," it poisons the earth in the garden of perplexity, so as to keep people away from Christ, and, in this case, worship the saints instead.
Another example: Free Will does not mean, "not a programmed robot." It means, "no longer in bondage to sin." The world wants you to believe that the true church claims that we are all pawns that God moves around on a chessboard. If you believe in the correct definition of free will and that Christ frees our wills from the bondage of sin, the fruits of revelation will rapidly grow in the garden.
Other examples abound: election, predestination, the trinity. In all cases we must go to the scriptures that rightly present the perplexities and give us the revelation by the Holy Spirit to be satisfied Christians. Whether you're Thomas and need just a nudge of revelation to believe or Saul, hater and persecutor of the church, who needs to be blinded and thrown down on the road to Damascus to believe, Christ will open your eyes to his truth when you are in honest perplexity.