Thomas Brooks emphasizes that the transformation of a holy Christian is the greatest miracle, illustrating how God opens the eyes of the blind to see sin and Christ, gives deaf ears the ability to hear His call, and enables the dumb to speak for Him. He describes the once lame who now runs towards God's commands and the dead who are made alive through faith in Christ. This miraculous change reflects a profound shift from a life of sin to one of holiness, showcasing the power of God's grace in a believer's life.