Note that $\triangle APB \cong \triangle BQC.$ Then, it follows that $\overline{PB} \cong \overline{QC}.$ Thus, $QC = PB = PR + RB = 7 + 6 = 13.$ Define $x$ to be the length of side $CR,$ then $RQ = 13-x.$ Because $\overline{BR}$ is the altitude of the triangle, we can use the property that $QR \cdot RC = BR^2.$ Substituting the given lengths, we have \[(13-x) \cdot x = 36.\] Solving, gives $x = 4$ and $x = 9.$ We eliminate the possibility of $x=4$ because $RC > QR.$ Thus, the side length of the square, by Pythagorean Theorem, is \[\sqrt{9^2 +6^2} = \sqrt{81+36} = \sqrt{117}.\] Thus, the area of the square is $(\sqrt{117})^2 = 117,$ so the answer is $\boxed{\textbf{(D) }117}.$
Note that there is another way to prove that $CR = 4$ is impossible. If $CR = 4,$ then the side length would be $\sqrt{4^2 + 6^2} = \sqrt{52},$ and the area would be $52,$ but that isn't in the answer choices. Thus, $CR$ must be $9.$
~NH14 ~sl_hc
Extra Note: Another way to prove $4$ is impossible. The side length of the square, $S$, is equal to $\sqrt{4^2 + 6^2} = \sqrt{52}$. Because $x = 4$, $RQ = 9$. Because $QB = \sqrt{RB^2 + RQ^2} = \sqrt{6^2 + 9^2} = \sqrt{117}$ and $QB  \sqrt{52}$, we have proof by contradiction. And so $x = 9$.
~ Wiselion (Extra Note)
In square $ABCD$, points $P$ and $Q$ lie on $\overline{AD}$ and $\overline{AB}$, respectively. Segments $\overline{BP}$ and $\overline{CQ}$ intersect at right angles at $R$, with $BR = 6$ and $PR = 7$. What is the area of the square?

$\textbf{(A) }85\qquad\textbf{(B) }93\qquad\textbf{(C) }100\qquad\textbf{(D) }117\qquad\textbf{(E) }125$