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The crew of the supply ship E.S.S Ariga receive a old distress call related to Nanostray infection, deciding to investigate it's origins and maybe reverse-engineer it to find a cure. The SHN-4 fighter is sent to Teppeki Dock, from where the distress call came, to investigate further. They manage to collect data on the first three outbreaks of the virus, so the SHN-4 is again sent to collect samples.
Further analysis reveals the Nanostray originated from military experiments from almost 70 years before the game's events, which were officially stopped back then. They finally track down the virus's origin to Himuro Base, which was overrun by hostile machines due to the Nanostray influence. The SHN-4 fights it's way through the base, facing against Nohkan, the so-called "patient zero". By destroying Nohkan, the entire place collapses and explodes.