Traditional dark matter models, e.g., weakly interacting massive particles (WIMPs), assume dark matter (DM) is weakly coupled to the standard model so that elastic scattering between dark matter and baryons can be described perturbatively by the Born approximation; most direct detection experiments are analyzed according to that assumption. We show that when the fundamental DM-baryon interaction is attractive, dark matter-nucleus scattering is nonperturbative in much of the relevant parameter range. The cross section exhibits rich resonant behavior with a highly nontrivial dependence on atomic mass; furthermore, the extended rather than pointlike nature of nuclei significantly impacts the cross sections and must therefore be properly taken into account. The repulsive case also shows significant departures from perturbative predictions and also requires full numerical calculation. These nonperturbative effects change the boundaries of exclusion regions from existing direct detection, astrophysical and CMB constraints. Near a resonance value of the parameters the typical velocity-independent Yukawa behavior, $\ensuremath{\sigma}\ensuremath{\sim}{v}^{0}$, does not apply. We take the nontrivial velocity dependence into account in our analysis, however it turns out that this more accurate treatment has little impact on limits given current constraints. Correctly treating the extended size of the nucleus and doing an exact integration of the Schr\"odinger equation does have a major impact relative to past analyses based on the Born approximation and naive form factors, so those improvements are essential for interpreting observational constraints. We report the corrected exclusion regions superseding previous limits from XQC, CRESST Surface Run, CMB power spectrum and extensions with Lyman-$\ensuremath{\alpha}$ and Milky Way satellites, and Milky Way gas clouds. Some limits become weaker, by an order of magnitude or more, than previous bounds in the literature which were based on perturbation theory and pointlike sources, while others become stronger. Gaps which open by correct treatment of some particular constraint can sometimes be closed using a different constraint. We also discuss the dependence on mediator mass and give approximate expressions for the velocity dependence near a resonance. Sexaquark ($uuddss$) DM with mass around 2 GeV, which exchanges QCD mesons with baryons, remains unconstrained for most of the parameter space of interest. A statement in the literature that a DM-nucleus cross section larger than ${10}^{\ensuremath{-}25}\text{ }\text{ }{\mathrm{cm}}^{2}$ implies dark matter is composite, is corrected.