The late nonlinear stages of laminar-turbulent transition in a three-dimensional flat plate boundary-layer are investigated by a highly-resolved temporal numerical simulation. The simulation is adapted to a transition experiment which allows a direct comparison of the obtained physical phenomena. The stationary crossflow vortex is the characteristic structure of the flow in the early transitional stage of the three-dimensional boundary-layer. The interaction of this vortical structure with travelling waves in presence of the wall is investigated. Different methods for the identification of vorticesare used. A new vortical structure is obtained in the present investigation. It finally destroys the primary crossflow vortex and initiates the onset of turbulence. The new vortical structure is also predicted by the investigation of the secondary stability of the nonlinear deformed crossflow vortex. The new vortical structure is located in a region with high shear and a high velocity defect of the velocity profile near the edge of the boundary-layer. It is shown that the secondary disturbance has a high temporal amplification rate and represents a high-frequency instability, which was observed likewise in the corresponding experiments. The spatial location of occurrence of the high frequency instability and their frequency agrees very well with the experiment.