Neither is good and necessary consequence a license to do whatever we want with the Bible, turning it into a wax nose for us to shape as we please. Just because we know that the entire Bible points to Christ (Luke 24:27) does not mean that the Father wants us to find Him in every step of the House of the Forest of Lebanon. However, it does mean that the one God of Israel subsists in the persons of the Father, the Son, and the Holy Spirit, and that the eternal order among the divine persons is the reason that God works from the Father, through the Son, by the Spirit, so that by one Spirit, we might come to the Father through Jesus Christ (Eph. 2:18). It also means that the God who purchased the church with His own blood (Acts 20:28) is the Son of God, who cannot suffer and die, who became man, who can. That God is triune and that Christ is the second person of the Trinity incarnate, with two distinct natures in one divine person, are not just good conclusions that are compatible with Scripture. They are necessary deductions, without which everything else in Scripture falls to pieces.
Only by listening both to what the Bible says and to what the Bible assumes are we able to understand clearly the whole counsel of God. While doing so will take prayer, the Spirit’s help, and plain hard work, God expects no less from us. The good news is that the Father promises to give the Holy Spirit to those who ask (Luke 11:13), and He is the same Spirit who opened the understanding of the disciples to comprehend the Scriptures (Luke 24:45). Even this point illustrates deducing the thought processes assumed by Scripture, since the Spirit is not mentioned explicitly in the Luke text, but Paul tells us in 2 Corinthians 3 that we can understand the Bible only through faith in Christ, and that it is the Spirit who unveils our eyes.
Together, express statements and deductions by good and necessary consequence press us to listen to the Bible as a whole. We should not be like children who break a window through carelessness, excusing themselves because their parents never told them not to break that window in particular. We need to read the Bible with eyes and ears attuned to who God is, how we know Him, and what He wants us to believe and do. We learn these things as much from our overarching relationship to Him as we do from the express statements and examples He gives us.
This leads to a broader point that Westminster Confession 1.6 does not lose sight of. We need to know how to interpret Scripture properly, but we need more than this. Understanding what God says and means is not enough: “The inward illumination of the Spirit of God [is] necessary for the saving understanding of such things as are revealed in the Word.” We need to be taught by God in our hearts (John 6:47), as the same Spirit who teaches us what to believe in the Word enables us to receive Christ in the Word through sincere faith (1 Cor. 2:12–14). The God who spoke in creation, bringing light out of darkness, must shine in our hearts, enabling us to know the light of the glory of God in the face of Jesus Christ (2 Cor. 4:6).
While we might not understand everything in Scripture with equal clarity, sometimes not hearing what God is saying, yet the sheep hear the Good Shepherd’s voice (John 10:27). Do we know the triune God’s character, and do we recognize Him and His will behind and around Bible texts as well as in what He spells out for us explicitly?