A mesogen-substituted polydiacetylene which self-assembles into stacks of bilayered two-dimensional structures was investigated by X-ray and electron diffraction as well as electron microscopy. The multilayered stacks of bilayers were found to organize into single crystals with an orthorhombic unit cell. Within each two-dimensional structure, the polyconjugated backbones are oriented along either of the two ab plane face diagonal directions, and the substituted side chains are oriented parallel to the layer normal (c-axis direction). The layered single-crystal structures form blue solids at room temperature but undergo the well-known thermochromic and solvatochromic transitions which produce red, orange, and yellow solids. In this work we have established links among chromic transitions, molecular organization, and morphology of these two-dimensional assemblies. Their thermochromic transition from blue to red solids at elevated temperature was found to be accompanied by reversible fracturing of the large single crystals. However, the red to orange transition at even higher temperatures was found to be associated with the irreversible twisting of fractured crystals and the lengthening of the chemical repeat. Based on electron diffraction, this twisting is accompanied by rotations of mesogenic side chains substituting the polydiacetylene backbone. On the other hand, our studies suggest that conformational changes do not play a role in the reversible blue to red transitions of these two-dimensional assemblies. Electronic delocalization perpendicular to the backbone may be a factor in these reversible changes linked to the fracturing of crystals.