On Earth-616, a familiar tragedy weighs heavily on Peter Parker. Still haunted by the death of his Uncle Ben, Spider-Man fights alongside the Avengers against Doctor Doom in New York City. When a building collapses despite his efforts, Peter is devastated. Tony Stark tries to teach him that a hero cannot save everyone, but Peter refuses to accept that sacrifices are necessary. Exploiting the young hero's despair, Doctor Doom questions the very nature of heroism before launching a missile strike. Just as Doom moves in for the kill, a mysterious phantom train phases into reality. This is the Train of the Vary Dimension, a cosmic vehicle first seen in Ultra Q that carries lost souls through the multiverse. Both Spider-Man and the stowaway Doctor Doom are swept away.

Doom kicks Peter off the train, sending him plummeting into an unfamiliar version of Tokyo, Japan. This is a world where giant monsters called kaiju rampage through cities and humanity is protected by a silver giant of light. Peter watches in awe as Shin Hayata transforms into Ultraman to battle a giant lizard kaiju named Peter. Unlike the cynical MCU he left behind, this new world offers a different philosophy. Spider-Man is a street-level hero driven by guilt to save every single person, but he struggles with the binary choice of saving the few versus the many. Ultraman, while possessing god-like power, believes in protecting all life, even the kaiju. He teaches Peter that conflict does not always require destruction.

Meanwhile, Doctor Doom finds himself stranded in the Land of Light as well. He craves the power of the Giant of Light and forms a dark alliance with the cunning Alien Mefilas, who commands an army of monsters from the Monster Graveyard. Together, they launch experiments to break the heroes' spirits, focusing on the transformative power of desire.

The first major arc pits Spider-Man and Ultraman against the brainwave kaiju Gango, discovered by a lonely, bullied boy named Onita. Gango has the ability to transform into anything the human mind conceives. Onita, filled with resentment, wishes for revenge, turning the harmless creature into a weapon. Gango copies Spider-Man's powers, and Onita uses it to attack his schoolmates and parents. Spider-Man must confront a dark mirror of himself: a child with power but no sense of responsibility. In a poignant climax, Peter explains to Onita that with great power comes great responsibility, teaching the boy that kindness, not force, defines a hero. The act of kindness transforms Gango not into a monster, but into the image of Uncle Ben, allowing Peter a moment of emotional catharsis.

This victory is short-lived. Doctor Doom enters the fray. Having finally stolen the power of Ultraman for himself, he transforms into a monstrous, god-like figure reminiscent of his infamous Secret Wars appearance. Stripped of his power, Shin Hayata reverts to a dying state, prepared to sacrifice the last of the Ultra's energy to save his own life. Alien Mefilas, realizing Doom intends to rule Earth rather than share it, turns on his ally, unleashing kaiju like Gomora and Red King to stop him. As Doom easily smashes through these monsters, the narrative delves into Victor Von Doom's tragic past. Having lost his mother to a demonic pact and his father to a tyrant's cruelty, Doom seeks absolute power to control fate itself.

The story reaches its conclusion as a depowered Peter Parker must carry a dying Shin Hayata to safety. With Tokyo in ruins and a power-mad Doctor Doom declaring himself king of a new "Land of Light," Spider-Man and Ultraman must find a way to stop him without the power to fight him directly. The series explores whether human connection and reciprocal acts of kindness can heal trauma as deep as Doom's, or if the cycle of violence can only be broken by rejecting the binary of fight or flight in favor of understanding.