It's odd the stain is on the roof but not the vent/refrig/AC covers. Those vent covers look new. I would guess it was parked near a tree last fall and leaves sat on the roof over winter to rot.
If it is leaves on an EPDM rubber roof, I would just wash it once or twice a year with Spic-n-span and the roof will 'calk off' the stain. You should notice improvement by this fall or next year.
Tom and Amy from Northern Virginia.
2000 Allegro 454/Workhorse P32/TST/Crossfire
Life is a DIY project - enjoy it.