Heteroepitaxial Ge 0.98 Mn 0.02 quantum dots on Si (001) were grown by molecular beam epitaxy. The standard Ge wetting layer-hut-dome-superdome sequence was observed, with no indicators of second phase formation in the surface morphology. We show that Mn forms a dilute solid solution in the Ge quantum dot layer, and a significant fraction of the Mn partitions into a sparse array of buried, Mn-enriched silicide precipitates directly underneath a fraction of the Ge superdomes. The magnetic response from the ultra-thin film indicates the absence of robust room temperature ferromagnetism, perhaps due to anomalous intermixing of Si into the Ge quantum dots.