A three-dimensional simulation of hovering flapping wings was performed using an immersed boundary method. This was done to investigate the effects of chordwise wing deformation on three important unsteady aerodynamic mechanisms found in flapping flight, namely Leading Edge Vortex (LEV) shedding, wake capture and clap and fling. A wing was modeled as a flat plate, flapping close to a symmetry plane. Three different deforming chords were defined, a rigid case, a case with maximum deformation at the trailing edge and increased angle of attack (AoA) near the leading edge, and a case with the maximum deformation in the center of the chord and decreased AoA near the leading edge. All cases had zero deformation at the wing root and maximal deformation at the wing tip. A higher AoA near the leading edge resulted in faster LEV buildup and faster buildup of lift. No shedding of the LEV was observed in any of the cases even when deformation caused a high AoA near the leading edge. A distinct dip in lift buildup was observed and shown to be caused by the interaction between the previously shed vortex and the newly developing LEV. This interaction occurred faster when the AoA at the leading edge was increased, and slower when the angle of attack was decreased. Moving the wing closer to the symmetry plane had a positive effect on the cycle average value of CL. This positive effect was reduced however by the earlier interaction between the LEV and the previously shed vortex.