In this paper we extend the hierarchical model reduction framework based on reduced basis techniques for the application to nonlinear partial differential equations. The major new ingredient to accomplish this goal is the introduction of the adaptive empirical projection method, which is an adaptive integration algorithm based on the (generalized) empirical interpolation method. Different from other partitioning concepts for the empirical interpolation method we perform an adaptive decomposition of the spatial domain. We project both the variational formulation and the range of the nonlinear operator onto reduced spaces. Those reduced spaces combine the full dimensional (finite element) space in an identified dominant spatial direction and a reduction space or collateral basis space spanned by modal orthonormal basis functions in the transverse direction. Both the reduction and the collateral basis space are constructed in a highly nonlinear fashion by introducing a parametrized problem in the transverse direction and associated parametrized operator evaluations, and by applying reduced basis methods to select the bases from the corresponding snapshots. Rigorous a priori and a posteriori error estimators, which do not require additional regularity of the nonlinear operator are proven for the adaptive empirical projection method and then used to derive a rigorous a posteriori error estimator for the resulting hierarchical model reduction approach. Numerical experiments for an elliptic nonlinear diffusion equation demonstrate a fast convergence of the proposed dimensionally reduced approximation to the solution of the full-dimensional problem. Runtime experiments verify a close to linear scaling of the reduction method in the number of degrees of freedom used for the computations in the dominant direction.