As a compressor is throttled three-dimensional separations develop in the corners between the blades and annulus endwall. Surprisingly, little is understood about the unsteady topology of these separations. One of the problems with studying corner separations is that it is often difficult to understand whether a particular flow structure in the separation is inherent to the separation itself, or due to the response of the separation to changes in the inlet flow. In this paper a novel experimental approach is taken with the aim of isolating the corner separation from external influences. A cascade is designed with the specific aim of precisely controlling the inlet flow. Contrary to previous work, it is shown that the key saddle and focus pair, which describes the time-mean topology of the corner separation on the endwall, moves smoothly and continuously as the incidence of the flow is raised. This behavior is shown to be the result of the time-resolved topology of the flow field, which comprises numerous saddle and focus pairs which are produced stochastically in regions of high shear strain rate. Most importantly, the separation is shown to exhibit an extremely low frequency behavior, changing in topology over timescales which are approximately 80 times the convection time through the blade passage. The behavior is shown to be intrinsic to the separation and causes the separation, for periods, to completely disappear from the endwall. This underlying unsteady structure of the separation is shown to have implications for the ability of RANS-based design codes to be able to accurately predict corner separations.