We introduce and study the notion of a generalised Hecke orbit in a Shimura variety. We define a height function on such an orbit and study its properties. We obtain lower bounds for the sizes of Galois orbits of points in a generalised Hecke orbit in terms of this height function, assuming the ‘weakly adelic Mumford–Tate hypothesis’ and prove the generalised André–Pink–Zannier conjecture under this assumption, using Pila–Zannier strategy.

In his 1982 paper, Ogus defined a class of cycles in the de Rham cohomology of smooth proper varieties over number fields. This notion is a crystalline analogue of $\ell$-adic Tate cycles. In the case of abelian varieties, this class includes all the Hodge cycles by the work of Deligne, Ogus, and Blasius. Ogus predicted that such cycles coincide with Hodge cycles for abelian varieties. In this paper, we confirm Ogus’ prediction for some families of abelian varieties. These families include geometrically simple abelian varieties of prime dimension that have non-trivial endomorphism ring. The proof uses a crystalline analogue of Faltings’ isogeny theorem due to Bost and the known cases of the Mumford–Tate conjecture.