Let $X$ be a set. Then, $\operatorname{Mor}_{\mathbf{Set}}(X,\{ 0,1\} )$ is a Boolean ring. In fact, it is a complete atomic Boolean ring and this, together with the the cofunctor from complete atomic Boolean rings to sets $\operatorname{Mor}_{\mathbf{Ring}}({-},\mathbb{Z}/2\mathbb{Z})$ yields a coequivalence of categories between the category of sets and the category of complete atomic Boolean rings---see pg. 26 of Khalkhali's Basic Noncommutative Geometry.
On the other hand, classic Stone Duality says that the category of Boolean rings is coequivalent to the category of Stone spaces, the cofunctors implementing the equivalence being given by $\operatorname{Spec}$ and $\operatorname{Clopen}$ (the functor that takes a topological space to its Boolean algebra of clopen sets)---see Lurie's notes.
I now claim that $\operatorname{Mor}_{\mathbf{Ring}}({-},\mathbb{Z}/2\mathbb{Z})$ is naturally isomorphic to $\operatorname{Spec}({-})$, the natural isomorphism being given by $$ \operatorname{Mor}_{\mathbf{Ring}}(B,\mathbb{Z}/2\mathbb{Z})\ni \phi \mapsto \operatorname{Ker}(\phi )\in \operatorname{Spec}(R). $$ sending a homomorphism $B\rightarrow \mathbb{Z}/2\mathbb{Z}$ to its kernel. (I am regarding them as functors from the category of Boolean rings into $\mathbf{Set}$.) The quotient of a Boolean ring is Boolean ring. Furthermore, the only Boolean ring that is an integral domain is $\mathbb{Z}/2\mathbb{Z}$. Thus, for $\mathfrak{p}\in \operatorname{Spec}(R)$, we must have that $R/\mathfrak{p}\cong \mathbb{Z}/2\mathbb{Z}$. $$ \operatorname{Spec}(B)\ni \mathfrak{p}\mapsto (B\rightarrow B/\mathfrak{p})\in \operatorname{Mor}_{\mathbf{Ring}}(B,\mathbb{Z}/2\mathbb{Z}) $$ then gives us an inverse to $\phi \mapsto \operatorname{Ker}(\phi )$. I will spare you the check of naturality.
Putting these facts together, we have $$ X\cong \operatorname{Mor}_{\mathbf{Ring}}(\operatorname{Mor}_{\mathbf{Set}}(X,\{ 0,1\} ),\mathbb{Z}/2\mathbb{Z})\cong \operatorname{Spec}(\operatorname{Mor}_{\mathbf{Set}}(X,\{ 0,1\} )), $$ $\cong$ here meaning ``naturally isomorphic as endofunctors on $\mathbf{Set}$''. However, Stone Duality says that the right-hand side comes equipped with a canonical Stone (in fact, Stonean) topology (namely the Zariski topology). This suggests that every set has a canonical Stonean topology. I can only think of a couple of topologies one can define on any set (discrete, indiscrete, cofinite) and none of them seem to be Stonean in general.
I imagine there is a flaw in my understanding somewhere, but I'm afraid I am not seeing where. Can someone help point out what I'm missing?
Additionally, after clearing that up, it would be nice to know the following.
Is there a concrete characterization of the topological spaces that are of the form $\operatorname{Spec}(\operatorname{Mor}_{\mathbf{Set}}(X,\{ 0,1\} ))$?
For example, von Neumann algebras also give Boolean rings (their Boolean algebras of projections), and there is a relatively concrete description of the spaces which correspond to these Boolean rings. Can do we do the same for those Boolean rings that arise as the power set of some set?