The loss of axisymmetry in a swirling flow that is generated inside an enclosed cylindrical container by the steady rotation of one endwall is examined numerically. The two dimensionless parameters that govern these flows are the cylinder aspect ratio and a Reynolds number associated with the rotation of the endwall. This study deals with a fixed aspect ratio, height/radius = 2.5. At low Reynolds numbers the basic flow is steady and axisymmetric; as the Reynolds number increases the basic state develops a double recirculation zone on the axis, so-called vortex breakdown bubbles. On further increase in the Reynolds number the flow becomes unsteady through a supercritical Hopf bifurcation but remains axisymmetric. After the onset of unsteadiness, another two unsteady axisymmetric solution branches appear with further increase in Reynolds number, each with its own temporal characteristic: one is periodic and the other is quasi-periodic with a very low frequency modulation. Solutions on these additional branches are unstable to three-dimensional perturbations, leading to nonlinear modulated rotating wave states, but with the flow still dominated by the corresponding underlying axisymmetric mode. A study of the flow behaviour on and bifurcations between these solution branches is presented, both for axisymmetric and for fully three-dimensional flows. The presence of modulated rotating waves alters the structure of the bifurcation diagram and gives rise to its own dynamics, such as a truncated cascade of period doublings of very-low-frequency modulated states.