The growth of InGaN on GaN (0001) by plasma-assisted molecular beam epitaxy was investigated with special focus on the dynamics of the formation of the dots. A metastable 2D growth regime, where the surface changes from smooth to rough by thermal treatment during growth interruption, existed previous to the 2D-3D transition. Both small regular-shaped dots and large irregular-shaped islands were observed. The large islands were suppressed by choosing correct growth conditions. The critical thickness for the transition from 2D to 3D growth also depended on the growth conditions. The growth of GaN capping layer to cover InGaN dot-structure was also attempted.