In issue #20, the title received a minor makeover, officially joining the 2099 imprint and changing its name to X-Men 2099 A.D., the "A.D." standing for "After Doom".

In June 2009, a mini-series called Timestorm 2009–2099 brought back Spider-Man, Ghost Rider, the X-Men, and more from the 2099 universe in a very different version.

The team featured an ever-changing line-up, but the mainstays included: The series was written entirely by John Francis Moore and pencilled almost exclusively by Ron Lim.

The other members are Meanstreak (now a young girl), Krystalin, Junkpile (now a self-replicating Stark android), and Bloodhawk (now female, and with a touch that "can give life, or take it", similar to Xi'an).

[2] When the time traveling mutant Tempus ends up in the year 2099, she meets a new version of X-Men 2099 consisting of Desert Ghost, Skullfire, Meanstreak, Metalhead, Serpentina & Sham.