Jesus, the Son, is the second Person of the Trinity. He has the same nature as God the Father and God the Holy Spirit, and yet Jesus is different in that He is fully God and at the same time fully man. Such a mystery, that God would choose to identify with us in this way!
From eternity, Jesus preexisted with the other two members of the Godhead. He is not younger than the Father, for neither of them ever had a beginning. But there came a time in human history when Jesus identified with mankind by becoming one of us. He has a beginning as a human being — a miraculous beginning: conceived and born of a virgin by the power of the Holy Spirit. We call His beginning as a human the Incarnation. Isaiah had prophesied centuries before, “Therefore, the Lord himself shall give you a sign: behold, a virgin shall conceive and bear a son, and shall call his name Immanuel [God with us]” (Isaiah 7:14).
Let’s talk a bit about Jesus’ conception. It seems to be a stumbling block for many, but if we are going to believe that God is all-powerful and can do every other kind of miracle, then there should not be any question of Jesus’ ability to be conceived supernaturally, either. We must be clear on the facts: God the Father did not have a sexual liaison with Jesus’ mother Mary. If He had, it would not have been a virgin birth. In pagan culture, we often find myths of gods interacting sexually with earthly women out of their own lusts, but what we must remember is that those pagan gods actually have demon entities behind them. The stories are based on demon behaviors that have actually taken place in the earth at various times. The True and Living God does not behave in these ways.
The angel Gabriel told Mary, “The Holy Spirit shall come upon you, and the power of the Highest shall overshadow you: therefore that holy thing which shall be born of you shall be called the Son of God” (Luke 1:35). Joseph, Mary’s future husband, described in the Bible as “a just man,” was distraught to hear that Mary was expecting a child, and “the angel of the Lord appeared to him in a dream, saying, ‘… do not fear to take Mary as your wife: for that which is conceived in her is of the Holy Spirit'” (Matthew 1:20). The understanding, for both Mary and Joseph, was that no sexual union had taken place between God and Mary. Jesus’ conception was a supernatural event.
What does it mean then, you might ask, that Jesus is the “only begotten Son of the Father”? 1 John 4:9 gives us a hint: “In this, the love of God was manifested toward us: that God sent his only begotten Son into the world, that we might live through him.” Jesus, already referred to as the only begotten Son, is sent. The begetting came before the sending. Jesus is the only begotten Son of the Father from eternity, without a beginning point — again, without any sexual union having accomplished this. We are not able to understand how this could be, but must accept it as one of the many unfathomable mysteries of who God is.