Lyric discussion by explorer12 

Cover art for Pluto lyrics by Sufjan Stevens

The song is a mix of Roman mythology and astronomic information about Pluto. "Jupiter bad June" (My favorite part in whole song) could refer to the fact that Jupiter has married with his own sister, Juno. Jupiter is also the brother of Pluto in the Roman mythology. "Charon, the fog lifted/ Messenger dwarfism", Charon is the name of the biggest moon in Pluto, it has half of size of the planet. And Pluto is known for being a dwarf planet. Sworn by Persephone/ Our melancholy/ She waits forever in your kiss - Persephone in Roman mithology is the Pluto's wife that was kidnapped. The rest of the song I have no idea what is it about :], that's my opinion, I can be totally wrong.

My Interpretation