In this paper a theoretical study is undertaken to investigate the structure of the lower branch neutral stability modes of three-dimensional small disturbances imposed on the incompressible Von Karman’s boundary layer flow due to a rotating disk. Particular attention is given to the short-wavelength non-linear non-stationary cross-flow vortex modes at sufficiently high Reynolds numbers with reasonably small scaled frequencies. Following closely the asymptotic frameworks introduced in [Proc. Roy. Soc. London Ser. A 406 (1986), 93–106] and [Proc. Roy. Soc. London Ser. A 413 (1987), 497–513] for the stationary linear and non-linear modes, it is revealed here that the non-stationary modes with sufficiently long time scale can also be described by an asymptotic expansion procedure based on the triple-deck theory. Making use of this approach, which takes into account the non-linear and non-parallel effects, the asymptotic structure of the non-stationary modes is shown to be adjusted by a balance between viscous and Coriolis forces, and resulted from the fact of vanishing shear stress at the disk surface. As a consequence of the matching of the solutions in adjacent regions it is found that in the linear case the wavenumber and the orientation of the lower branch modes are governed by an eigenrelation, which is akin to the one obtained previously in [Proc. Roy. Soc. London Ser. A 406 (1986), 93–106] for the stationary modes. The asymptotic theory shows that the non-parallelism has a destabilizing effect. A Landau-type equation for the modulated vortex amplitude with coefficients that are often difficult to get from finite Reynolds number computations has also been obtained from a weakly non-linear analysis in the limit of infinitely large Reynolds numbers. The non-linearity has also been found to be destabilizing for both positive and negative frequency waves, though finite amplitude growth of a disturbance having positive frequency close to the neutral location is more effective.