The narrative begins with the mysterious "Metro Flood," where impossible railway bifurcations appear in Tokyo's subway system, leading to its shutdown and the disappearance of investigators. This phenomenon, attributed to "Super Fungi," consumed Tokyo a century ago, transforming it into a "fungal plant paradise" and giving rise to "Shin-Tokyo."
Abe Shuu, a 23-year-old salaryman, awakens naked and disoriented in a fungus-covered underground chamber, his severe injuries from a recent fall miraculously healed. He stumbles into a dilapidated subway tunnel, soon identified as the "Ootsuka Metro" on its 50th floor. Attacked by a giant "Ghost Wolf," Shuu instinctively manifests a "fungal sword" from his palm, killing the beast, and discovers his "Regeneration Kin'nou" (fungal ability) as his bitten arm instantly heals.
Overwhelmed, Shuu is found by Tamiko, a talking, squirrel-like "Carbuncle" (majuu) with a gem on her head. She explains the post-apocalyptic world, identifies Shuu as a "Hunter" (Karyuudo) and one of the "Thread-spinning people" (Itokuri no Tami) capable of Kin'nou. Tamiko instructs him to eat the wolf's "fungal sacs" (houshinou) for "level-ups," which Shuu reluctantly does, gaining strength. Tamiko, having lived alone since her mother's death, offers to guide Shuu to the surface, a world she yearns to see. They form a partnership, establishing a hidden base and discovering an "oasis" for resources. Shuu learns to manifest his fungal sword at will and begins hunting weaker "Metro Beasts" like rats, but Tamiko stresses the need for stronger foes like Ghost Wolves and "Goblins" (evolved apes) for significant growth.
Their first major challenge arises when Shuu and Tamiko ambush a battle between a Ghost Wolf and Goblins. Shuu, despite sustaining severe injuries, defeats the wolf. A surviving Blue Goblin then attacks, forcing Shuu to awaken a new Kin'nou: the "Burning Fungal Orb," which explodes on impact, securing his victory. Over the next six months, Shuu diligently hunts, developing his combat skills and acquiring a "Fungal Shield" at level 7. He reaches level 17 (Tamiko is 14), mastering his four Kin'nou (Regeneration, Fungal Sword, Burning Fungal Orb, Fungal Shield). They learn about other powerful Metro Beasts, including peaceful "Unicorns" and terrifying "Wraiths."
During a scouting mission into Goblin territory, they trigger a "Bell-Run" plant, alerting a pack of Goblins. While fleeing, they are cornered by the Goblins and then by a formidable "Wraith," a top-tier Metro Beast (estimated level 50+). The Wraith easily overpowers Shuu, inflicting critical injuries. Tamiko bravely intervenes, activating her "Fungal Shell" Kin'nou, but is severely wounded. Enraged, Shuu unleashes multiple Burning Fungal Orbs directly into the Wraith's mouth, causing a massive explosion that allows them to escape. Back in their hideout, Shuu instinctively uses his fifth Kin'nou, a "White Fungal Orb," to heal Tamiko, discovering its potent restorative properties.
As Tamiko recovers, she tearfully confesses a crucial secret: the true obstacle to the surface is the "Boss" of the 49th floor, an indestructible "Slime" that killed her mother's hunter partner. This revelation, coupled with the traumatic Wraith encounter, hardens Shuu's resolve. Despite the overwhelming odds, he reaffirms his commitment to Tamiko, vowing to grow strong enough to overcome all challenges and reach the surface world together.
