The X-Men had the same origins as 616, up until the present day (2013). In the present day, the X-Men started pairing up together and having children. Sometimes it was consensual. Sometimes not so much (see Mercury). When the Skrulls touched down on Earth, all X-Men were retired, had lost their powers, or had died. But a new generation of mutant X-Men stood, prepared for the threat.
A New Generation
After the media predicted another apocalyptic event (ironically, by Apocalypse), the realization of just how long they had been doing the hero business began sinking in. They began having children, attempting part of a normal life. However, most of the parents still continued to be X-Men. The kids were raised with frequent combat training with their powers, but most aspects of their life were normal.In a strong contrast to the Avengers, the X-Men children were all raised together. Their founding roster consisted of White Wolf, Howl, Chill (now Brain Freeze), Rook, Hell's Angel, and Shadowcrawler. They debuted fighting a new mutant Sinister Six to fight the X-Men. They were a successful team, and this made them cocky, even after Howl left, but after fighting the Skrulls, they knew humility.
Skrull Rescue Squad
Soon, the news worldwide broadcast footage of a Skrull ship docked in Earth's atmosphere. The ship dispatched Wave Alpha: 4 of its best agents, specially created to capture the Avengers and X-Men. These agents captured the X-Men. Brain Freeze was able to escape along with Iron Knight, and she went and formed a new X-Men team to free the others. She recruited Deathshriek, Beast II, X-Bandit, Yeti, and Psi-Lord. He telepathically reached Mystery and Mercury, and SolarStorm rounded out the line-up. Again led by Shadowcrawler, the team entered space, and soon made quick work of Wave Alpha. The other waves were easy to defeat. Upon returning home, some people left, but most of them stayed. After all, the world would always need, and have, X-Men.