Red Skull commands Hydra as its primary antagonist, manipulating four genetically enhanced teenagers—Makoto, Adi, Chloe, and Bruno—through rigorous training that frames the Avengers as villains. He exploits their powers to advance Hydra’s objectives, with his central ambition revolving around the hazardous "Emerald Rain Project," an undisclosed initiative posing a major threat. During a clash with the Avengers at a Hydra base, Red Skull employs nanomachine armor to amplify his physical prowess but is ultimately overpowered and captured. The base’s self-destruction triggers Bruno’s apparent demise and Makoto’s sudden emergence of emerald wings, both events intrinsically linked to the unresolved Emerald Rain Project.

Imprisoned on the Raft, Red Skull survives an assassination attempt during transfer when the Winter Soldier, acting on orders from Hydra’s covert allies—the Masters of Evil—targets him to prevent interrogation. The Avengers thwart the assault, securing Red Skull’s continued incarceration and exposing his ties to this broader villainous network. Despite confinement, his alliance with the Masters of Evil endures, driving their ongoing pursuit of the Emerald Rain Project’s goals. The project’s connection to Makoto’s emerald wings persists, signaling Red Skull’s schemes remain active beyond his imprisonment, with no definitive resolution to his plans or fate.