To start the "Cloud Altas" mystery, you just have to reach the Nazi Meteorological Station in Gizeh. You'll find it just west of the Great Sphinx and south of the Nazi Recreation Area near the center of the map.
The logbook lists a series of times and types of clouds. The atlas page has the types of clouds associated with numbers. To find the code, you have to take the handwritten times at the bottom of the Cloud Atlas Page, and reference them against the Cloud Status Logbook.
On the Cloud Status Logbook page, these times have Cirrus, Stratus, Cirrus, and Cumulonimbus observed. Back on the Cloud Atlas Page, these become the code for the chest in the other room - 0609.
Open the chest to find some cash and the Gizeh Medicine exploration book.
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