A single polycrystalline diamond aggregate from the Orapa kimberlite (Botswana) contains a syngenetic micro- and nano-inclusion suite of magnetite, pyrrhotite, omphacite, garnet, rutile and C-O-H fluid in order of abundance. This suite of inclusions is distinctly different from those in fibrous diamonds, although the presence of sub-micrometer fluid inclusions provides evidence for a similarly important role of fluids in the genesis of polycrystalline diamond. It is the first study of polycrystalline diamond by High resolution μ-CT (Computed Tomography) reaching a resolution of 1.3 μm using polychromatic X-rays. Combined with Focused Ion Beam assisted Transmission Electron Microscopy the method reveals epigenetic replacement coatings of hematite and late stage sheet silicates around the magnetites showing that magnetites are often (but not always) interstitial to the diamond and, thus, were open to late stage overprinting. It is proposed that the polycrystalline diamond formed by a redox reaction between a small-scale carbonatitic melt and a sulfide-bearing eclogite. The water released from the melt during diamond precipitation fluxed local melting of the surrounding eclogite, and oxidation of sulfide phases to magnetite, which mingled with the carbonatitic melt and (re-)precipitated locally.