Let $f(x) = x^2 + 6x + c$ for all real numbers $x$, where $c$ is some real number.  For what values of $c$ does $f(f(x))$ have exactly $3$ distinct real roots?
Suppose the function $f(x) = 0$ has only one distinct root.  If $x_1$ is a root of $f(f(x)) = 0,$ then we must have $f(x_1) = r_1.$  But the equation $f(x) = r_1$ has at most two roots.  Therefore, the equation $f(x) = 0$ must have two distinct roots.  Let them be $r_1$ and $r_2.$

Since $f(f(x)) = 0$ has three distinct roots, one of the equations $f(x) = r_1$ or $f(x) = r_2$ has one distinct root.  Without loss generality, assume that $f(x) = r_1$ has one distinct root.  Then $f(x) = x^2 + 6x + c = r_1$ has one root.  This means
\[x^2 + 6x + c - r_1\]must be equal to $(x + 3)^2 = x^2 + 6x + 9 = 0,$ so $c - r_1 = 9.$  Hence, $r_1 = c - 9.$

Since $r_1$ is a root of $f(x) = 0,$
\[(c - 9)^2 + 6(c - 9) + c = 0.\]Expanding, we get $c^2 - 11c + 27 = 0,$ so
\[c = \frac{11 \pm \sqrt{13}}{2}.\]If $c = \frac{11 - \sqrt{13}}{2},$ then $r_1 = c - 9 = -\frac{7 + \sqrt{13}}{2}$ and $r_2 = -6 - r_1 = \frac{-5 + \sqrt{13}}{2},$ so
\[f(x) = x^2 + 6x + \frac{11 - \sqrt{13}}{2} = \left( x + \frac{7 + \sqrt{13}}{2} \right) \left( x + \frac{5 - \sqrt{13}}{2} \right) = (x + 3)^2 - \frac{7 + \sqrt{13}}{2}.\]The equation $f(x) = r_1$ has a double root of $x = -3,$ and the equation $f(x) = r_2$ has two roots, so $f(f(x)) = 0$ has exactly three roots.

If $c = \frac{11 + \sqrt{13}}{2},$ then $r_1 = c - 9 = \frac{-7 + \sqrt{13}}{2}$ and $r_2 = -6 - r_1 = -\frac{5 + \sqrt{13}}{2},$ and
\[f(x) = x^2 + 6x + \frac{11 + \sqrt{13}}{2} = \left( x + \frac{7 - \sqrt{13}}{2} \right) \left( x + \frac{5 + \sqrt{13}}{2} \right) = (x + 3)^2 + \frac{-7 + \sqrt{13}}{2}.\]The equation $f(x) = r_1$ has a double root of $x = -3,$ but the equation $f(x) = r_2$ has no real roots, so $f(f(x)) = 0$ has exactly one root.

Therefore, $c = \boxed{\frac{11 - \sqrt{13}}{2}}.$