With his mathematical writings it was the same story. Others questioned his methods, and rather than treating these questions as part of the normal scientific give and take, Newton got offended and claimed he would "let what I write ly by till I am out of ye way." Indeed, he said he was going to put philosophy aside and "prosecute some other subjects."
What were these other subjects that had grabbed Newton's attention? They were two: alchemy and theology.
Newton's obsession with alchemy, which lasted many more years than did his brief fascination with mathematics, seems strange to us from the viewpoint of the 21st century. It helps to remember that two of his known correspondents on the subject were that master experimentalist Robert Boyle and the arch empiricist John Locke. In 1672, the idea that chemical substances contained spiritual principles and could, under the right circumstances, vegetate and grow, was not so obviously unscientific as it appears today.
Newton obtained his alchemical writings from a secret network about which we know very little today. Many alchemists hid their names, publishing under pseudonyms. Newton referred to them in his writings by initials alone. Newton amassed a vast collection of alchemical manuscripts over a period of more than 30 years.
He was not just reading about alchemy, though: he built his own laboratory, with an impressive variety of furnaces to produce the various levels of heat he needed for his experiments. In spite of the length of time he spent on these investigations and his copious notebooks, it is not so clear what his goal in all this was. Producing gold appears very rarely as a target. A more definite goal was something he called "sophic sal ammoniac." At one point in his notes he becomes very excited at the idea that he has succeeded in producing this mysterious substance.
I perfected the ideal solution. That is, two equal salts carry up Saturn. Then he carries up the stone and joined with malleable Jupiter also makes X [a star symbol I can't reproduce here] and that in such proportion that Jupiter grasps the scepter. Then the eagle carries Jupiter up. Hence Saturn can be combined without salts in the desired proportions so that fire does not predominate. At last mercury sublimate and sophic sal ammoniac shatter the helmet and the menstruum carries everything up.
The passage gives you a feel for what alchemical writing was like: coded, allusive, and mysterious. Surely, a man of Newton's intelligence and skills would not have wasted his time for three decades on complete nonsense! To him, it must have meant something: what that was, we can no longer recover.