Laminar separation bubbles generated on a flat plate by an adverse pressure gradient are investigated using direct numerical simulations (DNSs). Two-dimensional periodic forcing is applied at a blowing/suction slot upstream of separation. Control of separation through forcing with various frequencies and amplitudes is examined. For the investigation of absolute instability mechanisms, baseflows provided by two-dimensional Navier–Stokes calculations are analysed by introducing pulse disturbances and computing the three-dimensional flow response using DNS. The primary instability of the time-averaged flow is investigated with a local linear stability analysis. Employing a steady flow solution as baseflow, the nonlinear and non-parallel effects on the self-sustained disturbance development are illustrated, and a feedback mechanism facilitated by the upstream flow deformation is identified. Secondary instability is investigated locally using spatially periodic baseflows. The flow response to pulsed forcing indicates the existence of an absolute secondary instability mechanism, and the results indicate that this mechanism is dependent on the periodic forcing. Results from three-dimensional DNS provide insight into the global instability mechanisms of separation bubbles and complement the local analysis. A forcing strategy was devised that suppresses the temporal growth of three-dimensional disturbances, and as a consequence, breakdown to turbulence does not occur. Even for a separation bubble that has transitioned to turbulence, the flow relaminarizes when applying two-dimensional periodic forcing with proper frequencies and amplitudes.