The alchemy side of Newton. http://www.hypatiamaze.org/isaac/newton.html
Newton’s conception of the physical world provided a stable model of the natural world that would reinforce stability and harmony in the civic world. Newton saw a monotheistic God as the masterful creator whose existence could not be denied in the face of the grandeur of all creation. “The beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent Being. […] This Being governs all things, not as the soul of the world, but as Lord over all; and on account of his dominion he is wont to be called “Lord God” παντοκρατωρ [pantokratōr], or “Universal Ruler”. […] The Supreme God is a Being eternal, infinite, [and] absolutely perfect .
Although the laws of motion and universal gravitation became Newton’s best-known discoveries, he warned against using them to view the Universe as a mere machine, as if akin to a great clock. He said, “Gravity explains the motions of the planets, but it cannot explain who set the planets in motion. God governs all things and knows all that is or can be done.”
Newton refashioned the world governed by an interventionist God into a world crafted by a God that designs along rational and universal principles .
Newton was a monotheist who believed in biblical prophecies but was Antitrinitarian. In Newton’s eyes, worshipping Christ as God was idolatry, to him the fundamental sin. (what does Newton think about Jesus?) Historian Stephen D. Snobelen says of Newton, “Isaac Newton was a heretic. But … he never made a public declaration of his private faith—which the orthodox would have deemed extremely radical. He hid his faith so well that scholars are still unravelling his personal beliefs .
The young Newton did not aspire to ecclesiastical orders requisite for the mastership of a college. His theological interests, however, were not an aberration of old age. All his life he was a conforming member of the Anglican Church, although he had reservations about its Trinitarian doctrine. Although he appreciated its universalist humanitarianism, he was by no means a deist inasmuch as he believed in a personal God, omniscient and omnipotent, but, above all, immanent not only had He created the universe, but He keeps it under constant surveillance and intervenes in a providential way from time to time (e.g., paths of comets). Neither was Newton a Unitarian; he believed in Jesus Christ as the Messiah, the Son of God-not a mere man, but a sort of viceroy for the Father (his precise concept is somewhat problematic). Newton diligently sought the Creator through His actions, His work (creation) and His Word (the Bible). – http://www.adherents.com/people/pn/Isaac_Newton.html
Newton wrote more on religion than he did on natural science. Newton himself may have had some interest in millenarianism as he wrote about both the Book of Daniel and the Book of Revelation in his Observations Upon the Prophecies. In a manuscript he wrote in 1704 in which he describes his attempts to extract scientific information from the Bible, he estimated that the world could end (no earlier than) on 2060. In predicting this he said, “This I mention not to assert when the time of the end shall be, but to put a stop to the rash conjectures of fanciful men who are frequently predicting the time of the end, and by doing so bring the sacred prophesies into discredit as often as their predictions fail.”
Sir Isaac Newton (1642–1727), the noted English scientist and mathematician, wrote many works that would now be classified as occult studies. These occult works explored chronology, alchemy, and Biblical interpretation (especially of the Apocalypse). Newton’s scientific work may have been of lesser personal importance to him, as he placed emphasis on rediscovering the occult wisdom of the ancients. During Newton’s lifetime the study of chemistry was still in its infancy, so many of his experimental studies used esoteric language and vague terminology more typically associated with alchemy and occultism. Western alchemy is recognized as a protoscience that contributed to the development of modern chemistry and medicine. Alchemists developed a framework of theory, terminology, experimental process and basic laboratory techniques that are still recognizable today. But alchemy differs from modern science in the inclusion of Hermetic principles and practices related to mythology, religion, and spirituality.
 Principia, Book III; cited in; Newton’s Philosophy of Nature: Selections from his writings, p. 42, ed. H.S. Thayer, Hafner Library of Classics, NY, 1953.
 Frankel, Charles (1948). The Faith of Reason: The Idea of Progress in the French Enlightenment. New York: King’s Crown Press. p. 1.
 Snobelen, Stephen D. (1999). “Isaac Newton, heretic: the strategies of a Nicodemite”. British Journal for the History of Science 32 (4): 381–419.