Ishihara Toru is an everyday guy with an on-and-off girlfriend and a position working for a train buff. Things become complicated when a ghostly vehicle dubbed the X Train begins to ride the rails, destroying everything in its path. Somehow, it seems that Toru is connected with the X Train by a strange power, which draws the attention of some very dangerous and power hungry people who would wield it for their own...

解体を数日後に控えた電気機関車ＥＦ５８６１が、突如姿を消した――。主人公の水原トオルは、地下鉄の駅のホームで消えた電気機関車ＥＦ５８６１に偶然遭遇。するとトオルの身体に異変が起きてしまうのだった。列車とトオル、この二つを結ぶ謎とは一体何なのだろうか……？