Because of the high-magnitude earthquake and consequent tsunami that struck the east coast of Japan on March 11, 2011, at 14:46, Tokyo Electric Power Company's Fukushima Daiichi nuclear power plant experienced station blackout (SBO) resulting in a nuclear accident unprecedented in time and extent. Simulation of such an accident by means of computer codes is largely dependent on the applied boundary conditions and physical models. However, still-unknown boundary conditions and unclear phenomena result in uncertain computed quantities. In this study, first, the boundary conditions of emergency systems are theoretically derived, starting from a discussion of the reactor available measured quantities and related uncertainties. Then, newly implemented physical models (e.g., wetwell condensation mechanism), which were not accounted for in historical studies of long-term SBOs, are explained. As an early method for accident clarification and explanation regarding effective boundary conditions, results from the SAMPSON severe accident code were compared with theoretical values. The results of SAMPSON compared with the measured quantities available have shown that despite successful safety operations performed by the plant operators in Fukushima Daiichi Unit 3, the eventual lack of batteries (for systems operation and measurement reading) led to plant conditions of low core water level at high pressure, nullifying the attempt of the subsequent alternative water injection to prevent core degradation.