What follows does not account for every detail and folio, and is subject to change without notice.
The Voynich Manuscript is a private work encompassing the Author’s ideas of Life, the Universe, and Everything. It is encoded because he felt he had found a Great Truth, and wanted it kept to himself.
The Rosettes foldout, f86, is the centerpiece, a map showing places and things of importance.
It is oriented with East at the top, as indicated by the right-side-up (rising) sun in the upper left, and the upside-down (setting) sun in the lower right. A T-O map in the upper right corner confirms the orientation. T-O maps are also used for orientation on folios f67v2 and f68v3.
The top center, middle left and right, and bottom middle circles are astronomical, while the remaining outside circles are terrestrial. The middle circle is the access to the Biological Section.
The upper right circle has a castle, some other buildings, and a beach between them and the waves crashing in.
The lower right circle has a field and jars from the Pharmaceutical section. This is where the plants in the Herbal section are grown and processed.
The Biological Section, i.e. the Bathing Nymphs, encompasses the sciences of Meteorology, Hydrology and the metascience of Alchemy.
At the top of folios f75r, f78r, and f79v is the earth’s surface, with water running off underground where the Nymphs renew it and send it out again, as envisioned by the system of pipes around them and on the Rosettes foldout.
Rain is falling at the top of f84v, and is controlled and directed by Nymphs, as seen on f79v, f80v, f83r and f83v.
Folio f85r2 shows the cycle of time; birth, life, death, renewal.
Folio f68v3 shows how the Universe rotates around the earth.
The Astronomical section shows two comets, a total solar eclipse, four planetary conjunctions, a supernova (anomalous to the dating of the other events), and an important conjunction of the moon with stars in the Aries/Taurus region.
The Zodiac section lays out those events against the signs using a graphical coding. The Zodiac starts with Pisces because that sign is involved with the events, and it would be inconvenient to have it at the other end of the section. Aries and Taurus are split to allow more room for the events depicted.
The Recipes section is an Almanac, as suggested by Glen Claston.