We show the problem of counting homomorphisms from the fundamental group of a homology $3$-sphere $M$ to a finite, non-abelian simple group $G$ is #P-complete, in the case that $G$ is fixed and $M$ is the computational input. Similarly, deciding if there is a non-trivial homomorphism is NP-complete. In both reductions, we can guarantee that every non-trivial homomorphism is a surjection. As a corollary, for any fixed integer $m ge 5$, it is NP-complete to decide whether $M$ admits a connected $m$-sheeted covering. Our construction is inspired by universality results in topological quantum computation. Given a classical reversible circuit $C$, we construct $M$ so that evaluations of $C$ with certain initialization and finalization conditions correspond to homomorphisms $pi_1(M) to G$. An intermediate state of $C$ likewise corresponds to a homomorphism $pi_1(Sigma_g) to G$, where $Sigma_g$ is a pointed Heegaard surface of $M$ of genus $g$. We analyze the action on these homomorphisms by the pointed mapping class group $text{MCG}_*(Sigma_g)$ and its Torelli subgroup $text{Tor}_*(Sigma_g)$. By results of Dunfield-Thurston, the action of $text{MCG}_*(Sigma_g)$ is as large as possible when $g$ is sufficiently large; we can pass to the Torelli group using the congruence subgroup property of $text{Sp}(2g,mathbb{Z})$. Our results can be interpreted as a sharp classical universality property of an associated combinatorial $(2+1)$-dimensional TQFT.
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