When Eva Bell traveled to an alternate 2099 future, Skullfire was among the X-Men she encountered. This Tim appeared to be wearing more traditional make-up for his skull visage rather than the dermal bonding mask worn by the original Fitzgerald. His history with the X-Men 2099 is otherwise unknown.
During Civil War II, Spider-Man 2099 visited an alternate version of his 2099 timeline. This world operated under the restrictions of the Anti-Powers Act, making it illegal for superhumans to act outside the law. The origins of the rift are unknown, but Skullfire, Bloodhawk, and La Lunatica were seen as deputized superhumans under the Act, with Cerebra acting against them in the resistance.
In Heroes Reborn 2021, Skullfire appeared among the allies of Magneto and the Mutant Force. This version of Tim presumably traveled back in time and became stuck in the present of this alternate timeline, as so many other mutant heroes have done in the past.
In the Cross-Time Caper, the future Brotherhood traveled back into the past and posed as the O5 X-Men when they were stuck in the present. This created an alternate timeline where the original X-Men were viewed as the fascist founders of AlchemaX and their rigid control over 2099.
Skullfire led the resistance team of X-Men 2099 who opposed AlchemaX and fought to protect their people. With a new strain of Legacy Virus attacking the populace, the X-Men stole medicine from the rich to help those who couldn't help themselves. They crossed paths with the genuine original five members of the X-Men, who were jumping through time to avoid the timestorm caused by the Brotherhood's actions. The Beast later summoned Skullfire's X-Men back in time as reinforcements to help them defeat the Brotherhood and reset the timeline.