Even the biggest most vicious rooster on the planet is completely vulnerable and at the mercy of predators at night when chickens are virtually blind.
A pen, unless it is completely covered and of wood, metal and hardware cloth won't keep predators out. Mink and weasels can get through tiny openings, raccoons and opossum can climb - anything. And fox can climb/jump virtually any fence.
Pens don't keep owls and hawks out either.
Since the bird is gone except for a leg, that rules out mink, weasels and likely opossums.
Any of the others are capable of eating most of the bird in situ.
Depending on where you live, there may be others capable of that 'odd death'.
Now is a good time for you to get a nice rooster that won't attack you while you prepare your housing to eliminate nighttime predators.