The following contains spoilers for Marauders #4, now on sale from Marvel Comics
Since House of X and Powers of X, the X-Men have discovered plenty of secrets about the mutant race including lost nations of their kind, the machinations of their greatest allies, and the enemies that have always been preparing for them.
It's gotten to the point X-Men have sent the Marauders onto a further fact-finding mission about untold Shi'Ar secrets. Marauders #4 (by Steve Orlando, Eleonora Carlini, Matt Milla, and VC's Ariana Maher) reveals some key facts that could change the future for most of the Marvel Universe if it all comes to light.
The Marauders been uncovering an untold secret about the mutant race, hidden away by the Crimson Kin of the Shi'Ar Empire. It was such an important truth that their forces were even willing to kill their Empress Xandra to keep it hidden. But just because they crossed lines to keep it a secret doesn't mean they could actually keep the information out of mutant hands. After fighting their way through the armada (and losing Kate Pryde in the process), the remaining Marauders find a version of Fang who is reborn with the information whenever the Crimson Kin need him.
Psylocke and the formerly villainous Cassandra Nova then use their powers to reveal the secrets hidden within his mind. It turns out in the early days of the planet Earth, mutants were among the earliest races and may have actually been the first natural-born species of the planet to create a society. Their home, Threshold, could be seen as an ancient precursor to Krakoa and even predates Krakoa and Arakko. The civilization was a peaceful one for the most part, content to simply lead their lives until the Shi'Ar arrived at prehistoric Earth. At this point they were a space-faring race of pirates instead of an intergalactic empire, and their initial attack against the mutants was a fruitless one.
Their pride wounded, the early Shi'Ar prepared for a war, and tried to wipe out these ancient mutants only to lose again. Their defeat so overwhelming that they hid it from the annals of history. But the truth remained as they transformed into the Shi'Ar of the present day and when these early mutants were forced to flee Earth to avoid the cataclysmic events that the Avengers 1,000,000 BC faced, the Shi'Ar took the opportunity to wipe out most of the briefly vulnerable mutants as they attempted in other realities.
Only a handful of mutants survived, placed outside of time by the Shi'Ar. Even then they were seemingly executed by the Shi'Ar years previously, cutting off Krakoa from that piece of their history -- or rather they would be, if Tempo wasn't a part of the team and willing to go back a few years to rescue those long-lost mutants. The fact that mutants are that ancient is something of a game-changer for the Marvel Universe and could become important for a lot of reasons.
It undercuts the hateful human rhetoric that suggests mutants are actively trying to replace humanity as they've been around longer than humanity. If mutants are truly that old, they may be less tied to the Deviants than otherwise believed, throwing off Druig's plans in Judgement Day. A secret mutant society could also serve as a series of lessons for Krakoa, potentially imparting valuable insight that could salvage Krakoa from threats both inside and from outside.
These revelations could upend a lot of the politics that are motivating the battle between humans and mutants and could further jeopardize the alliance between the X-Men and the Shi'Ar. A secret nation of mutants is a potential game-changer if they're brought back into the modern-day and could seriously affect the future of the entire Marvel Universe.