Magnetic actuation of microscopic beads is a promising technique for enhancement and manipulation of scalar transport in micro-fluidic systems. This implies laminar and essentially three-dimensional (3D) unsteady flow conditions. The present study addresses fundamental transport phenomena in such configurations in terms of 3D coherent structures formed by the Lagrangian fluid trajectories in a 3D time-periodic flow driven by a rotating sphere. The flow field is represented by an exact Stokes solution superimposed by a nonlinear closed-form perturbation. This facilitates systematic "activation" and exploration of two fundamental states: (i) invariant spheroidal surfaces accommodating essentially 2D Hamiltonian dynamics; (ii) formation of intricate 3D coherent structures (spheroidal shells interconnected by tubes) and onset to 3D dynamics upon weak perturbation of the former state. Key to the latter state is emergence of isolated periodic points and the particular foliation and interaction of the associated manifolds, which relates intimately to coherent structures of the unperturbed state. The occurrence of such fundamental states and corresponding dynamics is (qualitative) similar to findings on a realistic 3D lid-driven flow subject to weak fluid inertia. This implies, first, a universal response scenario to weak perturbations and, second, an adequate representation of physical effects by the in essence artificial perturbation. The study thus offers important new insights into a class of flow configurations with great practical potential.