When the Fukushima nuclear power plant accident occurred in March of 2011, a hydrogen explosion in the reactor building at the 4th unit of Fukushima plants led to a big surprise because the full core of the unit 4 reactor had been moved and stored underwater at the spent nuclear fuel storage pool for periodic maintenance. It was because the possible criticality in the fuel storage pool by coolant loss may yield more severe situation than the similar accident happened inside the reactor vessel. Fortunately, it was assured to be evitable to an anxious situation by a look of water filled in the storage pool later. In the paper, the safety state of the spent fuel storage pool and rack structure. The impacts influenced on the performance and safety of a repository are classified as units of features, events, and processes, for the total system performance assessment related to the permanent disposal of HLW. The importance is evaluated in consideration of the frequency, consequence, regulation, suitability of a specific site, etc. A scenario describing the migration of radionuclide from the repository to the biosphere is derived from understanding the interaction among these groups.