We study, from the point of view of abelian and Kummer surfaces and their moduli, the special quintic threefold known as Nieto's quintic. It is, in some ways, analogous to the Segre cubic and the Burkhardt quartic and can be interpreted as a moduli space of certain Kummer surfaces. It contains 30 planes and has 10 singular points: we describe how some of these arise from bielliptic and product abelian surfaces and their Kummer surfaces.

Let $V$ be a $K3$ surface defined over a number field $k$. The Batyrev-Manin conjecture for $V$ states that for every nonempty open subset $U$ of $V$, there exists a finite set ${{Z}_{U}}$ of accumulating rational curves such that the density of rational points on $U\,-\,{{Z}_{U}}$ is strictly less than the density of rational points on ${{Z}_{U}}$. Thus, the set of rational points of $V$ conjecturally admits a stratification corresponding to the sets ${{Z}_{U}}$ for successively smaller sets $U$.

In this paper, in the case that $V$ is a Kummer surface, we prove that the Batyrev-Manin conjecture for $V$ can be reduced to the Batyrev-Manin conjecture for $V$ modulo the endomorphisms of $V$ induced by multiplication by $m$ on the associated abelian surface $A$. As an application, we use this to show that given some restrictions on $A$, the set of rational points of $V$ which lie on rational curves whose preimages have geometric genus 2 admits a stratification of Batyrev-Manin type.