Cooperativity is used by living systems to circumvent energetic and entropic barriers to yield highly efficient molecular processes. Cooperative structural transitions involve the simultaneous, concerted displacement of molecules in a crystalline material, in stark contrast to the more typical molecule-by-molecule nucleation and growth mechanism often breaking the single crystallinity. Cooperative transitions have acquired much attention in the research community for their low transition barriers, ultrafast kinetics, and structural reversibility. On the other hand, cooperative transitions are rarely observed in molecular crystals and the molecular origin is not well understood. Single crystals of 2-dimensional quinoidal terthiophene (2DQTT-o-B), a high-performance n-type organic semiconductor, demonstrate two thermally-activated, reversible phase transitions with one exhibiting a cooperative mechanism and the second exhibiting a nucleation and growth mechanism. In situ microscopy, single crystal and grazing incidence X-ray diffraction (GIXD), along with Raman spectroscopy suggest a reorientation of the alkyl side chains results in a cooperative transition behavior. On the other hand, the nucleation and growth transition is coincident with both side chain melting and the emergence of new spin-spin interactions between conjugated cores, confirmed through in situ electron paramagnetic resonance spectroscopy (EPR). This is the first observation of biradical interactions directly initiating a structural transition. Through studying these fundamental mechanisms, we establish alkyl chain conformation and disorder as integral to rationally controlling these polymorphic behaviors for novel electronic applications.