We study the motion of non-diffusive, passive particles within steady, three-dimensional vortex breakdown bubbles in a closed cylindrical container with a rotating bottom. The velocity fields are obtained by solving numerically the three-dimensional Navier–Stokes equations. We clarify the relationship between the manifold structure of axisymmetric (ideal) vortex breakdown bubbles and those of the three-dimensional real-life (laboratory) flow fields, which exhibit chaotic particle paths. We show that the upstream and downstream fixed hyperbolic points in the former are transformed into spiral-out and spiral-in saddles, respectively, in the latter. Material elements passing repeatedly through the two saddle foci undergo intense stretching and folding, leading to the growth of infinitely many Smale horseshoes and sensitive dependence on initial conditions via the mechanism discovered by šil'nikov (1965). Chaotic šil'nikov orbits spiral upward (from the spiral-in to the spiral-out saddle) around the axis and then downward near the surface, wrapping around the toroidal region in the interior of the bubble. Poincaré maps reveal that the dynamics of this region is rich and consistent with what we would generically anticipate for a mildly perturbed, volume-preserving, three-dimensional dynamical system (MacKay 1994; Mezić & Wiggins 1994a). Nested KAM-tori, cantori, and periodic islands are found embedded within stochastic regions. We calculate residence times of upstream-originating non-diffusive particles and show that when mapped to initial release locations the resulting maps exhibit fractal properties. We argue that there exists a Cantor set of initial conditions that leads to arbitrarily long residence times within the breakdown region. We also show that the emptying of the bubble does not take place in a continuous manner but rather in a sequence of discrete bursting events during which clusters of particles exit the bubble at once. A remarkable finding in this regard is that the rate at which an initial population of particles exits the breakdown region is described by the devil's staircase distribution, a fractal curve that has been already shown to describe a number of other chaotic physical systems.