Main characters Peter Parker/Spider-Man – Sent to the future by a determined Jake Gallows, Peter is captured by the Public Eye. He meets Miguel who recently became the new Spider-Man and worries for his safety.
Miguel O'Hara/Spider-Man 2099 – A highschool student attending Pym Academy and son of Alchemax scientist George O'Hara. Miguel was caught in an explosion caused by the time flux while in class experimenting a spider, causing particles from the spider to transfer onto Miguel, granting him spider powers. Although inexperienced, he dons the identity of Spider-Man.
Logan/Wolverine – Transported into the year 2099 by Jake Gallows while tracking down members of the Hand with Luke Cage, Logan ends up in a desert wasteland, once Washington D.C., where he is confronted by a group of
Hulks. Logan/Wolverine 2099 – The future version of Logan, who is now an old man with no hair who had lost his right arm due to his battles against the Hulks. He found a new race of mutants and recruits them to his
X-Men team. Their headquarters are in a former Mutant containment facility called Fort Dawson in
Maryland. Logan and his team are trying to rebuild
Baltimore, which was destroyed in a war, and must restore civilization and defend it against an army of mindless Hulks.
Jake Gallows/Punisher 2099 – An employee of Alchemax and law enforcer of the "Public Eye", Jake travels back in time and is responsible for sending both Spider-Man and Wolverine to 2099. He has a strong hatred for the Heroes and would not hesitate to kill them, as his family was killed by armed, men wearing X-Men masks. It is later revealed that his co-workers were responsible for his family's death because Gallows had previously testified about a crime.
Shakti Haddad/Cerebra 2099 – A mutant girl with brain-like hair who has the power to reveal someone's history, both past and future, through touch. Shakti met Peter while they were imprisoned. She escaped with Peter and met Miguel, who was testing his powers, and suggested the design of Miguel's Spider-Man costume.
Villains Tyler Stone – Alchemax's Chief Executive, Tyler approved the development of the "Chronosphere" system, which monitors all of society and was responsible for the history alterations made using Jake Gallows as the voice of Thor. He unintentionally caused the explosion which placed Kron, mostly in a Scorpion body.
Kron Stone/Scorpion 2099 – A high school bully and son of Alchemax's Chief Executive Tyler Stone. Kron was caught in the blast with Miguel while in his classroom, due to the blast from the time flux, unintentionally caused by his father and Jake in the past. He was exposed to the Scorpion's particles and has the Scorpion's appearance. The Announcer – A man who watches his combatants fight to the death in the Ultimate Combat Arena for public ratings. Responsible for coordinating most of the fights and mostly involves the Human Torch.
Other characters • George O'Hara – The father of Miguel O'Hara and a scientist of Alchemax, George has been taking care of his son since his wife died and is worried for Miguel's safety. George has growing suspicious about Tyler Stone and Lyla are doing with Chronosphere and tries to find out what he is planning. • Lyla – A holographic system and assistant of Alchemax CEO Tyler Stone, Lyla notifies him about the history alteration and its progress, Lyla also notifies George about his son, Miguel. She appears to know about the events involving the Chronosphere, which causes George to doubt her and Stone. She is shut down for three hours while George and his friends observe what is inside the chronosphere, and links with Jake Gallows. • Relur/Human Torch 2099 – An Atlantean with fire-based superhuman abilities and a combatant who has won countless victories in the underground arenas. He admires Miguel as he is the only one to have lasted longer than any of his prior opponents. He is one of the few Atlanteans to develop mutant powers, but because of his fire-based abilities, the other Atlanteans deemed him a threat, forcing Relur to escape to the surface world. •
Kenshiro Cochrane/Ghost Rider 2099 – Kenshiro first met Logan thinking he was one of Logan's children. He is revealed to be a part of an organization called O.R.B.I.T. •
Hulk 2099 – As opposed to the original Hulk 2099, Hulks have become a species, as a gamma bomb was dropped on Washington D.C., turning all into Hulks. In a desert wasteland formerly known as Washington D.C., many other Hulks appear to have targeted Wolverine, who was transported by Jake and first encountered them and survived. Throughout the years the Hulk population expanded, leaving a portion of food left for humans to eat. Since then both human forces and existing mutants have been fighting the Hulks to preserve the food. •
Henri Huang/Meanstreak – A mutant who can run as fast as Quicksilver and is part of Logan's new X-Men team. Meanstreak is an easy going person who enjoys the speed. •
Lemuel/Bloodhawk – A red winged mutant and another member of Logan's X-Men team. This version of Bloodhawk is female and has the ability to give life or take it with only a touch, similar to Xi'an. •
Ruth Kristen Porter/Krystalin – Another member of Logan's X-Men, Ruth has the ability to absorb pollution from the air, turn it into crystals and use them for offensive maneuvers, but has trouble aiming. •
Junkpile – An
android and bodyguard of the X-Men team, this version of Junkpile formerly belonged to Tony Stark before it was destroyed. It was later rebuilt and was given its own personality, similar to Tony's. •
Doctor Doom – First appeared near the end of
Timestorm 2009–2099: X-Men. Doom was contained in a facility, barely alive but nearing his end, in the Smithsonian in Washington, D.C., where he was found by Logan and Ghost Rider. In
Timestorm 2009–2099 #3, he gives Ghost Rider 2099 information to find Shakti Haddad in Manhattan. He then dies.
Minor characters • Dana D'Angelo – A classmate and love interest of Miguel, Dana is attracted to Kron Stone and is friends with Reilly and Xina. This version of Dana has light purple hair colour. • Xina – The girlfriend of Reilly and friend of Dana. Xina does not like having Miguel around, but has allowed him since he is with Dana and is somewhat a friend of Reilly. • Reilly – Xina's boyfriend and friends of Kron Stone. Reilly is somewhat of a friend of Miguel, but mostly hangs out with Kron because of their interest in sports. ==Editions==