Through experiments using two-dimensional particle-image velocimetry (PIV), this paper examines the nature of transition in a separation bubble and manipulations of the resultant breakdown to turbulence through passive means of control. An airfoil was used that provides minimal variation in the separation location over a wide operating range, with various two-dimensional modifications made to the surface for the purpose of manipulating the transition process. The study was conducted under low-freestream-turbulence conditions over a flow Reynolds number range of 28,000–101,000 based on airfoil chord. The spatial nature of the measurements has allowed identification of the dominant flow structures associated with transition in the separated shear layer and the manipulations introduced by the surface modifications. The Kelvin–Helmholtz (K-H) instability is identified as the dominant transition mechanism in the separated shear layer, leading to the roll-up of spanwise vorticity and subsequent breakdown into small-scale turbulence. Similarities with planar free-shear layers are noted, including the frequency of maximum amplification rate for the K-H instability and the vortex-pairing phenomenon initiated by a subharmonic instability. In some cases, secondary pairing events are observed and result in a laminar intervortex region consisting of freestream fluid entrained toward the surface due to the strong circulation of the large-scale vortices. Results of the surface-modification study show that different physical mechanisms can be manipulated to affect the separation, transition, and reattachment processes over the airfoil. These manipulations are also shown to affect the boundary-layer losses observed downstream of reattachment, with all surface-indentation configurations providing decreased losses at the three lowest Reynolds numbers and three of the five configurations providing decreased losses at the highest Reynolds number. The primary mechanisms that provide these manipulations include: suppression of the vortex-pairing phenomenon, which reduces both the shear-layer thickness and the levels of small-scale turbulence; the promotion of smaller-scale turbulence, resulting from the disturbances generated upstream of separation, which provides quicker transition and shorter separation bubbles; the elimination of the separation bubble with transition occurring in an attached boundary layer; and physical disturbance, downstream of separation, of the growing instability waves to manipulate the vortical structures and cause quicker reattachment.