''The modern system of astronomy is now so much received by all inquirers, and has become so essential a part even of our earliest education, that we are not commonly very scrupulous in examining the reasons upon which it is founded. It is now become a matter of mere curiosity to study the first writers on that subject.
David Hume, Dialogues Concerning Natural Religion (1779), Part II
In 1694, seven years after the first edition of Principia, Whiston, then a fellow of Cambridge University, became a devoted pupil of Newton, and two years later submitted to his master the manuscript of a book entitled New Theory of the Earth. The book was intended to replace the then popular Theory of the Earth (1681) by Thomas Burnet, and dealt with a theme with which Newton had been concerned for more than a score of years. This book contended that the cataclysm described in the Old Testament as universal Deluge was caused by the impact of a comet at the end of the third millennium B.C., and that up to the Deluge the solar year had the duration of 360 days only, yet the new calendar of 365 days had to wait to be introduced by Nabonassar (in 747 B.C.). These contentions were based mainly on historical evidence, whereas astronomical considerations were the main ground for suggesting that comets may become planets.
Newton was so impressed by Whiston’s work that from that moment he established a close scientific relation with him. The book was highly praised also by other contemporaries, John Locke among them.
In 1701 Whiston was appointed as a temporary substitute for Newton at Cambridge, and in 1703, when Newton resigned permanently from the Lucasian Chair of Mathematics, he recommended Whiston as uniquely worthy to be his successor. By 1713, when the second edition of the Principia was published, Newton’s feelings towards Whiston had changed radically. When in 1720 the astronomer Edmond Halley (1656-1742) and others proposed Whiston as a member of the Royal Society, Newton threatened that, should the members vote for Whiston’s admission, he would resign from the presidency of the Society. Whiston, who was deeply devoted to Newton, suggested that his candidacy not be pressed; he felt that the aging Newton was so violently disturbed by the issue that he might die 
[emphasis added EM]. Halley who one year and a half before the publication of Whiston’s New Theory of the Earth had read a paper before the Royal Society in which he had explained the Deluge by the impact of a comet, but had not printed it 'lest by some unguarded expression he might incur the censure of the sacred order', reacted to Newton’s gesture by publishing with thirty years of delay a memoir in the acts of the society. Historians of science gloss over this incident, which is vital for the understanding of the evolution of Newton’s thought. After 1710, when Whiston was dismissed from his teaching position because of heresy and then formally brought to trial before the body of bishops of the Church of England, he assumed more radical positions and came to disagree with Newton who was becoming more and more conservative.
Whiston’s contention was that the creation story told in Genesis should not be interpreted literally, but as referring to a process of progressive creation through several cosmic stages. Newton, who was at first sympathetic to Whiston’s religious and scientific views, came to be shocked by his radicalism, and turned towards a fundamentalist position. The concluding words of Opticks indicate that Newton, like others of his contemporaries felt that, if the traditional views of cosmic order were abandoned, the foundations of morality would be undermined. Furthermore, Newton felt that Whiston’s hypotheses would end by eliminating what he considered the chief argument for the existence of God, the argument from design, namely, the wise adaptation of the present frame of nature to the needs of living creatures, especially man.
Whereas the first edition of the Principia (1687) is essentially rationalistic in spirit and follows a positivistic method, theological preoccupations dominate the second edition (1713). Newton is bent on proving that the machinery of the world is such a perfectly contrived system that it cannot be the result of 'mechanical cause', but must be the result of an intelligent and consistent plan. In order to support further the story of Genesis that the world was created by a single act, he argued also that the world is stable and has remained unchanged since creation. But he could not prove this point, since he admitted that, according to his own theory, the gravitational pull among the several members of the solar system would tend to modify their orbits; hence, he begged the question and claimed that God in his providence must intervene from time to time to reset the clockwork of the heavens to its original state. This point of Newton’s doctrine is well known, for it was the object of sarcastic comments by Newton’s great rival in the mathematical field, Leibniz (1646-1716). As the letter observed, Newton cast God not only as a clockmaker, and a poor one at that, but also as a clock-repairman. 
Scholars have failed to notice that the refutation of Whiston’s doctrine was of major concern to Newton. In the Principia, he maintained that comets, far from being a disruptive element, contribute to the providential preservation of the original order: since a certain amount of the water of the Earth is steadily consumed by chemical combinations, the seas would not be preserved in their original state unless new water was provided by the exhalations of comets. The notion of the providential purpose of comets was further expanded in Newton’s time: the comets exist also for the purpose of supplying new fuel to the Sun which otherwise would gradually consume itself. One of the important popularizers of Newton’s ideas stresses that comets can perform these providential functions, but at the same time are providentially prevented from striking the Earth.
Biographies of Newton usually dismiss in a few lines his book The Chronology of the Ancient Kingdoms Amended (1728), to which he dedicated the last years of his life. They consider it the product of an irrelevant side activity; yet its purpose is clearly that of refuting Whiston’s hypotheses. Newton argues that evidence for the years of 365 days is as old as the year 887 B.C., and that even though this year was ‘scarcely brought into common use’ before this date, it was as old as the first astronomical observation of the Egyptians. However, these would have started only quite late, in 1034 B.C. The main purpose of the book is to contend that there was hardly any reliable history before the First Olympic Games in 776 B.C. In the first page the point is made that the ancient legends and traditions (the basis of Whiston’s argument for a cataclysm caused by a comet) are not a reliable source of information.
Newton believed that his cosmology, which he had summed up in the famous General Scholium of the second edition of the Principia, could not be accepted unless Whiston was refuted. For this reason, about three months after the appearance of the second edition, he wrote an essay (that lies unpublished at the British Museum) in which he answered the criticism advanced by William Lloyd (1627-1717), an intimate friend of Whiston, on the ground that the oldest calendars of the ancients are based on a solar year of 360 days. From what is known about this document it can be said that Newton gave a lame answer. He argued that if a calendar of 360 days had been in use without a system of intercalation for the five extra days, the official beginning of the seasons would have moved around the full year in a period of 70 years; since there is no trace of this 70 year cycle, this calendar cannot have existed. But the argument of Whiston and Lloyd was exactly that the solar year was about 360 days long and that therefore no intercalation was needed. Newton was begging the question by assuming that the solar year must have always consisted of 365 days.
In the works of Newton the doctrine of the eternal stability of the solar system is clearly presented as an assumption based not on scientific data but on faith in a providential order...
In the case of Newton we meet with the unique occurrence that for three centuries his admirers have fought battle after battle in order to prevent the publication of about nine-tenths of his scholarly work. Whiston was one of the first to clamour for the publication of Newton’s manuscripts, since he wanted to have an opportunity to refute his historical theories.
If all the manuscripts were published, what had been claimed by some scholars and was granted by Newton himself in some of his letters, would become evident: that science was not his main interest and that he conceived of it as an auxiliary to theology.
Newton believed that the astronomical revolution linked with the names of Copernicus and Galileo had destroyed the foundations of religious belief and that it was necessary to return to the medieval world view. He was a biblical fundamentalist who tried to prove, among other points, that the Bible contains prophecies of future history. His interest in science was a byproduct of his effort to prove that even science does not conflict with biblical religion.
The voluminous unpublished works of Newton deal with many topics from alchemy to politics, but theology has the lion’s share, followed next by ancient history. These unpublished works cannot be dismissed as occasional efforts. To them he dedicated more time than to his scientific writings. They are just as accurately argued and well finished. All his writings constitute a unified stream of thought of which the scientific production was only one aspect.''
Livio Catullo Stecchini, Inconstant Heavens (The Velikovsky Affair, pp. 91-99)
The Newton's Manuscripts Collection at the National Library of Israel, Jerusalem:
https://web.nli.org.il/sites/nli/english/collections/humanities/newton/pages/default.aspx
A New Theory of the Earth... London, 1696, R. Roberts for Benj. Tooke; 1st Edition; complete. Frontispiece of the Solar System, [iv], 7 plates, 388, [2], errata : 4 engraved-in text illustrations; 8vo. Stamped contemporary calf boards, beautifully replaced spine in full aged calf. FINE CONDITION.
Price: USD 5,000,000.00