This sequel to the Silent Mobius The Movie 1 continues the timeline of the flashback section of the first movie (Katsumis initial contact with AMP), using some more ideas and persons from the Manga, and being slightly less incompatible to the Silent Mobius series from 1998.

With reports of monsters terrorizing the reactor at Mount Nibel, the Shinra Electric Power Company dispatches their elite fighting force SOLDIER to investigate. Accompanied by fellow SOLDIER First Class Zack Fair and a small contingent of company guards, the war hero Sephiroth is to assess the condition of the Mako reactor at the behest of the company. In Nibelheim, the village that the reactor powers, Sephiroth discovers the source of the monsters and the origins of Shinra's legendary Jenova Project. Running through the woods months later, Zack is no longer the hero he once dreamt of becoming. He flees from the General Affairs Department of the Shinra Electric Power Company, better known as the Turks, who desperately seek to bury the evidence living within the two.

Despite the Ends’ attack on Verlina being successfully repelled, the war has not yet ended. With the monster armies regrouping, the Black King tightens his grasp on the already conquered territory. New conflicts erupt all across Orte, as its remaining forces struggle to retain control over long-oppressed demi-human races. While Ends grow more potent each day, Toyohisa Shimazu remains unconscious after heavy injuries suffered during the Battle of Verlina. Facing enemies on every side, humanity’s fate is still on a knife's edge.

The entire countryside comes to a halt midday to witness a rare solar eclipse that is rumored to allow the average person to see Mushi. Unable to avert their gaze, the air is full of awe and wonder—but those who know the Mushi are preparing for the eclipse's aftermath. Based on a prediction from Tanyuu Karibusa, the cursed recorder, Mushishi Ginko finds himself in a very unlucky farming village. Immediately following the solar eclipse, a strange black cloud begins to gather in the sky and blocks the sun once more. Suspecting it to be the work of a Mushi known as Hihami, Ginko seeks to liberate the village from perpetual darkness. However, it seems that not all of the villagers are eager to return to the light.