David Gregory appears to have indexed Folio C, along with Quarto A and Folio B, and in Oxford in late 1699 or early 1700, when he was gradually completing his magnum opus, the Astronomiae. His editorial rationale for these apparently random collections is obscure. The index descriptions show that Folio C was meant to encompass a huge cache of colleagues' papers in general science, some on the nature of science itself. Chiefly by or about Newton, and usually concerning the prevailing tension between his brand of investigation and that of Descartes, or else about whether calculus was invented in England or Germany. Besides Newton, contributors to this general science collection originally numbered Leibniz, Sloan, Menzies, Herbert Kennedy, Kepler, Fatio, Viviani, Pitcairne, Collins. There were particular thoughts on medical science, in a note from Pitcairne on muscles, one from Newton on natural acids, and some else's account of human teeth of monstrous dimensions. As well, there were three contributions by James Gregorie, one on human thought, another on the upper atmosphere, and the other his St Andrew's thesis. There is one epigram for an obituary of Dr Gresham.

The largest group of indexed papers in a specific discipline are those in pure mathematics. Their descriptions span quadrature, descent into curves and solids, solving angles by algebra, maxima and minima, geometry in general, game theory, limits, cycloids, cone sections, the Florentine problem, tangents, fluxions, curves, cubes, circles, the catenary curve, hyperbolas and parabolas and the area they cover, quadratics, indeterminate numbers, arithmetic (notably division), planes, ellipses, trigonometry (especially arcs and tangents and log curves), the infinite series, and multinomial expressions.

Authors' names included James Fenton, Craig, Tschurnhaus (sic), Wallis, Descartes, James Gregorie, Hooke, De Sluse, Diophantus, Pythagorus, De Witt, Euclid, Mercator, Huygens, Hudde, Collins, De l'Hopital, Barrow, Kepler, Archibald Pitcairne (concerning his jousting with Edinburgh maths professor John Young), and Campbell. Astronomy papers covered the sun's and moon's periods, planetary position (and a machine to show it), the Cassinian orbit, comets, procession of the equinox, tides, aequitation of days, dates and calendars, notes on Huygens' horologium, eclipses, the parallax measurement, charting the heavens, and gravity. Astronomical authors include Halley, Newton, Flamsteed, James Gregorie, and Wallis.

Notes on physics, theoretical and applied, were meant to cover optics (refraction, notably, and discovering foci in circular reflectors), mechanics and statics (inclined planes, for the most part, and centripital force and trajectories), hydrostatics (on specific gravity, on how 'nautical spirals' are hyperbolic, and on why ships maneuver as they do), and on how sound propagates under water. Gregory also included thoughts on pneumatic, hydrostatic, hydraulic, and barascopic machines and gauges, on microscopes, on a magic lantern he once saw, and on how we might explore the deep sea. Individual authors include Oliphant, Huygens, Michael Dary, Fatio, Newton, Halley, and Boyle.

Gregory's papers encompassed many subjects that were not directly scientific, relating to his wider career as scientist, teacher, and administrator. These consisted of records of quarrels with the Edinburgh visitation committee and with other colleagues, notes on the teaching of mathematics and navigation, some political remarks on the Scottish church and parliament (with a table of the descendants of James I), and a silver-alloying table for Scottish Mint. Subsequent additions to the collections, not listed in the indices, are even more varied. Their dates span his entire professional life. Because palaeographic evidence suggests that these pages were not stored carefully, Gregory may have meant them to be more a stack of back files than an orderly documentary record of anything. Numerous documents on the index have migrated to other caches of Gregory papers or have disappeared completely.