In the future, Jake Gallows is sent to the present by Alchemax CEO Tyler Stone to eliminate Superheroes. Gallows then uses a chrono-device to send Spider-Man and Wolverine to his own time, thereby altering the future. In the future, 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 similar 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, but he is then 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 of the 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 having the Spider, and Kron with the 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 a 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, now fully recovered, breaks out of his cell and retrieves his mask and web-shooters then escapes with Shakti and goes into hiding while being hunted by law enforcement. Within a week, Miguel develops new spider powers, obtained in the blast. Deciding one night 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 has their first encounter with the Scorpion (who they do not recognize as Kron) and manage to defeat him. 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. Unable to heed Spider-Man's word, Miguel wears the costume again and enters an underground arena as a combatant facing off against the Human Torch. Although Miguel is defeated, the Human Torch is impressed with Miguel's skills and offers to teach him how 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-interment 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 also gained some co-operation from certain human civilizations for support, and perform several 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 manage to kill several Hulks. When Ghost Rider arrives at the scene, 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 informs them that he plans to assist them before he dies.
While in imprisonment in the Arena Cell, both Miguel (Spider-Man) and Relur (the Human Torch) reveal to each other their identity. 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 his reason for being there. After their discussion the two break out and escape. Meanwhile, George tricks Lyla and puts her out of commission for a few hours. He then manages to hack his way into the Chronosphere and is surprised to see that it shows Jack Gallows, but is even more surprised that he is in the past. When George tries to contact Jack, Jack believes that it is Thor contacting him, which makes George even more puzzled and gives him cause to question what Tyler was doing. While still searching for Shakti, Spider-Man sees both Miguel and Relur pass by and confronts Miguel as to why he's still wearing his Spider-Man costume. In the Smithsonian, Doctor Doom reveals to both Logan and Kenshiro that they must find Shakti in New York before he dies, but not before another time event is experienced. With the time stream badly damaged, both past and future eras begin to clash, causing individuals to crossover and leaving both Shakti and the Hulks in 2009 New York.