The Holy Spirit is baffling. That seems part of God's plan. Christians believe God's Spirit caused the inspiration of scripture and works to let us understand scripture as we read it. The first idea is called the doctrine of inspiration. This second point is the doctrine of illumination. We could think of the ancient monks who not only coped the words of scripture with immeasurable care and precision, they often drew pictures, or surrounded the text with design (The Book of Kells may be the most well know example). These were not just decorations. The art work is intended to help the reader understand the scripture more clearly, and to inspire devotion. The drawings are given to illuminate the meaning of the scripture. We believe the Holy Spirit illuminates the meaning of the scripture, as the ancient artists illustrated the scripture.
But the working of the Holy Spirit in Scripture itself is very puzzling. Luke tells us about Jesus' baptism (Luke 3): the heaven was opened, the Holy Spirit descended upon Jesus in bodily form like a dove. The strange descriptive 'bodily' surely must mean that the Spirit made himself visible to the eye. But the dove is a peculiar image. It might remind us of the dove that Noah sent our from the ark. It returned with a fresh olive leaf on its second journey. So the dove is an image of assurance. Or it may call to mind the doves that the very poor could use to participate in the sacrificial system of Ancient Israel. The dove is a clear but always unresolved assurance of God's presence. The Holy Spirit is definitely the presence of God, but never in a way that we can define absolutely. Like fog or smoke or the flames of a fire, the Spirit is present but in ways that are difficult to name.
Or we might take the curious work of the Spirit when Peter and John visit the new church in Samaria (Acts 8). Even though Jesus told his disciples they would carry the Gospel to the Samaritans, they likely looked on going to Samaria like we might consider being missionaries to aliens on another planet (thanks to Stan Mast for the wonderfully kooky link to books about Christian missionaries to other worlds!) The Spirit once again moves the church in surprising ways, and not for the last time. Peter and John lay hands on the new Christians. The work of the Spirit is so powerful that a local magician, Simon, attempts to purchase this power from the disciples. Why do we get no description of this manifestation of the Spirit? We do not learn what actually happens. Not only is that a curious choice by the author, it is spiritually puzzling. Does the Holy Spirit not want us to focus on the particulars of how God works in one group of believers? Is the passage meant to drive us to ask the Holy Spirit for gifts particular to our lives?