We define a notion of height for rational points with respect to a vector bundle on a proper algebraic stack with finite diagonal over a global field, which generalizes the usual notion for rational points on projective varieties. We explain how to compute this height for various stacks of interest (for instance: classifying stacks of finite groups, symmetric products of varieties, moduli stacks of abelian varieties, weighted projective spaces). In many cases, our uniform definition reproduces ways already in use for measuring the complexity of rational points, while in others it is something new. Finally, we formulate a conjecture about the number of rational points of bounded height (in our sense) on a stack $\mathcal {X}$, which specializes to the Batyrev–Manin conjecture when $\mathcal {X}$ is a scheme and to Malle’s conjecture when $\mathcal {X}$ is the classifying stack of a finite group.

We discuss the $\ell $-adic case of Mazur’s ‘Program B’ over $\mathbb {Q}$: the problem of classifying the possible images of $\ell $-adic Galois representations attached to elliptic curves E over $\mathbb {Q}$, equivalently, classifying the rational points on the corresponding modular curves. The primes $\ell =2$ and $\ell \ge 13$ are addressed by prior work, so we focus on the remaining primes $\ell = 3, 5, 7, 11$. For each of these $\ell $, we compute the directed graph of arithmetically maximal $\ell $-power level modular curves $X_H$, compute explicit equations for all but three of them and classify the rational points on all of them except $X_{\mathrm {ns}}^{+}(N)$, for $N = 27, 25, 49, 121$ and two-level $49$ curves of genus $9$ whose Jacobians have analytic rank $9$.

Aside from the $\ell $-adic images that are known to arise for infinitely many ${\overline {\mathbb {Q}}}$-isomorphism classes of elliptic curves $E/\mathbb {Q}$, we find only 22 exceptional images that arise for any prime $\ell $ and any $E/\mathbb {Q}$ without complex multiplication; these exceptional images are realised by 20 non-CM rational j-invariants. We conjecture that this list of 22 exceptional images is complete and show that any counterexamples must arise from unexpected rational points on $X_{\mathrm {ns}}^+(\ell )$ with $\ell \ge 19$, or one of the six modular curves noted above. This yields a very efficient algorithm to compute the $\ell $-adic images of Galois for any elliptic curve over $\mathbb {Q}$.

In an appendix with John Voight, we generalise Ribet’s observation that simple abelian varieties attached to newforms on $\Gamma _1(N)$ are of $\operatorname {GL}_2$-type; this extends Kolyvagin’s theorem that analytic rank zero implies algebraic rank zero to isogeny factors of the Jacobian of $X_H$.

Let $X$ be a curve over a number field $K$ with genus $g\geq 2$, $\mathfrak{p}$ a prime of ${ \mathcal{O} }_{K} $ over an unramified rational prime $p\gt 2r$, $J$ the Jacobian of $X$, $r= \mathrm{rank} \hspace{0.167em} J(K)$, and $\mathscr{X}$ a regular proper model of $X$ at $\mathfrak{p}$. Suppose $r\lt g$. We prove that $\# X(K)\leq \# \mathscr{X}({ \mathbb{F} }_{\mathfrak{p}} )+ 2r$, extending the refined version of the Chabauty–Coleman bound to the case of bad reduction. The new technical insight is to isolate variants of the classical rank of a divisor on a curve which are better suited for singular curves and which satisfy Clifford’s theorem.

We describe a probability distribution on isomorphism classes of principally quasi-polarized $p$-divisible groups over a finite field $k$ of characteristic $p$ which can reasonably be thought of as a ‘uniform distribution’, and we compute the distribution of various statistics ($p$-corank, $a$-number, etc.) of $p$-divisible groups drawn from this distribution. It is then natural to ask to what extent the $p$-divisible groups attached to a randomly chosen hyperelliptic curve (respectively, curve; respectively, abelian variety) over $k$ are uniformly distributed in this sense. This heuristic is analogous to conjectures of Cohen–Lenstra type for $\text{char~} k\not = p$, in which case the random $p$-divisible group is defined by a random matrix recording the action of Frobenius. Extensive numerical investigation reveals some cases of agreement with the heuristic and some interesting discrepancies. For example, plane curves over ${\mathbf{F} }_{3} $ appear substantially less likely to be ordinary than hyperelliptic curves over ${\mathbf{F} }_{3} $.