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Several possibilities could provide an answer as to why the moon would have charcoal-black surface patches, even though it is circling a dwarf planet that is as bright as freshly fallen snow. One theory that has been suggested proposes that, unlike larger objects such as Makemake, its own little companion moon is so small that it cannot gravitationally keep a grip onto a bright and icy crust, which then sublimates, undergoing a sea-change from solid to gas under the melting influence of warming sunlight. This would make the little moon akin to comets and other KBOs, many of which are well-coated with very dark material.
Furthermore, the icy stuff that collected on Methone's surface could even be more lightweight than that which lies beneath. It is possible that such fluffy, snowy, stuff can actually flow--at least over long periods of thousands to millions of years--thus filling in the tell-tale scars of impact craters.