Neurotransmitter release at the synapse requires fusion of synaptic vesicles with the presynaptic plasma membrane. SNAREs are the core constituents of the protein machinery responsible for this membrane fusion, but the actual fusion mechanism remains unclear. Here, we have simulated neuronal SNARE-mediated membrane fusion in molecular detail. In our simulations, membrane fusion progresses through an inverted micelle fusion intermediate before reaching the hemifused state. We show that at least one single SNARE complex is required for fusion, as has also been confirmed in a recent in vitro single-molecule fluoresence study. Further, the transmembrane regions of the SNAREs were found to play a vital role in the initiation of fusion by causing distortions of the lipid packing of the outer membrane leaflets, and the C termini of the transmembrane regions are associated with the formation of the fusion pores. The inherent mechanical stress in the linker region of the SNARE complex was found to drive both the subsequent formation and expansion of fusion pores. Our simulations also revealed that the presence of homodimerizations between the transmembrane regions leads to the formation of unstable fusion intermediates that are under high curvature stress. We show that multiple SNARE complexes mediate membrane fusion in a cooperative and synchronized process. Finally, we show that after fusion, the zipping of the SNAREs extends into the membrane region, in agreement with the recently resolved X-ray structure of the fully assembled state.