The fundamental flow physics of transition in uncontrolled and controlled separation bubbles for a modified NACA 643 − 618 airfoil at a chord Reynolds number of Re = 2 × 105 is investigated using a combined approach consisting of high-fidelity direct numerical simulations, linear stability analysis, and high-quality wind-tunnel experiments. For the uncontrolled flow, results from the DNS indicate a mean separation bubble that is larger than in the experiments, which may be explained by an earlier transition onset in the experiments caused by free-stream turbulence. In addition, active control of the laminar separation bubbles was investigated. Active flow control in the DNS is achieved by 2-D harmonic blowing and suction through a narrow spanwise slot, while the experiments use an alternating current dielectric barrier discharge plasma actuator. In both cases, the intent is to generate periodic 2-D disturbances upstream of the separation location. For the controlled flow, when forced with relatively small amplitudes, both experiment and DNS exhibit 3-D disturbance waves with distinct spanwise periodic structures that are generated inside the bubble near the maximum bubble height. Without additional (i.e., random) perturbations in the DNS (except the 2-D disturbances used for flow control), a delay of transition and even re-laminarization of the flow is demonstrated. By comparison of the DNS results with experimental data and stability theory, the dominant physical mechanisms for both the controlled and uncontrolled flows are identified.