Timestorm 2009–2099 is a four-issue mini-series, with two one-shots to give the story extra depth. These two one-shots focus on Spider-Man and Wolverine, with art by Wes Craig and Frazer Irving, respectively.
In the future, Jake Gallows is sent to the present by Alchemax CEO Tyler Stone to eliminate superheroes. Gallows uses a chrono-device to send Spider-Man and Wolverine to his own time, thereby altering the future. There, Miguel O'Hara meets with some of his friends (Kron Stone, Dana D'Angelo, Reilly and Xina) to see a combatant called the Human Torch at an underground arena. Elsewhere, Shakti Haddad is taken into custody by officers of the "Public Eye", wearing uniforms reminiscent of Jake Gallows'. In her cell, Shakti meets Spider-Man and realizes that he does not belong. Wolverine, meanwhile, finds himself in front of a group of Gamma-irradiated monsters. He is rescued by Kenshiro Cochrane, who mistakenly thinks he is one of Logan's children. While still imprisoned, Peter and Shakti experience another time event, altering some buildings in an explosion. At that precise moment, Miguel and classmate Kron Stone find themselves in the midst of that explosion, along with their experimented-upon insects (Miguel's Spider and Kron's Scorpion). In the hospital where Miguel and Kron are taken, George is glad to find that Miguel is alright, while Tyler is saddened and distressed that his son has not survived. With George and Miguel leaving, Tyler falls into tears having removed the sheet covering Kron's body, revealing that his son has the half mutated body of a scorpion. Tyler arranges for his son to be transferred to Alchemax in a tube, where his appearance cannot be seen.
Peter recovers, breaks out of his cell and retrieves his mask and web-shooters. He escapes with Shakti and goes into hiding while hunted by law enforcement. Within a week, Miguel develops new spider powers, obtained in the blast. Deciding to try his newfound powers, he falls due to a lack of confidence and is caught by Spider-Man, who is with Shakti.
Near them, an explosion issues from the Alchemax building. Spider-Man leaves to investigate and Miguel, in his own Spider-Man costume designed by Shakti, assists him. Inside the building, the team encounter and defeat the Scorpion (who they do not recognize as Kron). With the Public Eye's arrival at the scene, both Spider-Men are forced to stop them, but Miguel's father is left as a witness. In the aftermath, Spider-Man insists that Miguel get rid of his costume and stop acting as Spider-Man, fearing that he might be killed. Spider-Man then takes off, realizing that Shakti is missing. Without heeling Spider-Man's advice, Miguel wears the costume again and enters an underground arena as a combatant facing off against the Human Torch. Although Miguel is defeated, the Torch is impressed with his skills and offers to teach him to fight, but Miguel is unable to reply as the guards shock them unconscious.
In the meantime, Ghost Rider 2099 drops Logan in a former mutant-internment facility in a desert wasteland, formerly known as Maryland. There, Logan comes face-to-face with his future self, a bald old man with only his right arm, who now leads the new team of X-Men, headquartered at the facility. He also meets a new generation mutant named Henri Huang (code name Meanstreak) and robot bodyguard Junkpile, as well as two other mutants in the facility: Ruth Kristen Porter (Krystalin) and Lemuel (Bloodhawk).
Logan later discovers that the entire wasteland has been overrun by Hulks, who have eaten most of its food supplies and leave portions only for some civilizations, allowing others to starve. The X-Men have gained some co-operation from certain human civilizations for support, and perform joint operations against the Hulks as they attempt to restore a human civilization in Baltimore. When a group of human soldiers begins an assault against a group of Hulks, the X-Men, along with Logan, join the fight and kill several Hulks. When Ghost Rider arrives, the 2099 Logan asks Wolverine to go with him and find the one person that will help them. When Ghost Rider and Wolverine arrive at the Smithsonian in Washington D.C., they enter an old building and head towards the basement, where Wolverine is shocked to discover that Doctor Doom is there, barely alive. Doom reveals to Wolverine that both he and Spider-Man are in the future and that the timestream is in a state of chaos; he tells them that he plans to assist them before he dies.
While imprisoned in the Arena Cell, both Miguel (Spider-Man) and Relur (the Human Torch) reveal their identities to each other. Relur is one of the few existing Atlantian Mutants who were able to escape; he attributes his success to his fire ability; Miguel reveals his name and why he is there. After their discussion the two escape. Meanwhile, George tricks Lyla and puts her out of commission for a few hours. He then hacks into the Chronosphere and is surprised to see that it shows Jake Gallows, but is even more surprised that he is in the past.