ALTERNATE VERSIONS
Earth-928 originally concluded with a double-sized special, 2099: Manifest Destiny #1. Later stories retconned this into an alternate timeline, Earth-96943, allowing the original 2099 universe to continue.
By the beginning of 2100, humanity had reestablished colonies in the Savage Land and in the highest towers of New York City. Their reconstruction was aided by the return of the real Steve Rogers wielding the power of Mjolnir. When the Watcher arrived from the moon to alert humanity to the interdict barrier cutting their solar system off from the rest of the universe, La Lunatica and the heroes of Earth were assembled by Rogers into an ad hoc unit of Avengers to breach the barrier and reclaim the stars.
In one alternate version of 2099, the Anti-Powers Act was passed in America which made it illegal for superhumans to operate outside the law. La Lunatica, Skullfire, and Bloodhawk of the X-Men chose to become deputized under the Act to gain legitimacy, but they ended up hunting down Cerebra and other heroes of 2099 who refused to register.
In the Cross-Time Caper, the Brotherhood altered the past and created a new 2099 future, which was visited by the Original Five X-Men. They met the classic team of X-Men 2099, including Luna, fighting against the control of AlchemaX. A new version of the Legacy Virus threatened the populace, and the X-Men had to steal food and medicine from the haves to keep the have-nots alive.
In Savage Avengers, a time-travelling Deathlok lost his arm in the present era, leading to an 
alternate future of 2099 ruled by Ultron. This "Deathlok Prime" imprisoned most of the superhumans of that era until a team of Avengers arrived to undo his reign. Elektra Natchios helped free the prisoners, including mutants like La Lunatica and Bloodhawk, leading them in a revolution against machine rule.