Marvel's X-Men comics need to explore a secret mutant war that has been hinted at but never explored. The last few years have seen Marvel rewrite the history of the mutant race. It had previously been believed that, with the exception of occasional precursors, mutants were a recent evolutionary offshoot of the human race. Now it's clear mutants have existed since the dawn of time - with the first mutants seen 1,000,000 years ago.
This has opened the door to countless intriguing plots, shining a light on an aspect of Marvel history that's never been explored. The X-Men have learned the history of anti-magic violence was in part directed against mutants, and in fact Mordred - the son of King Arthur - was a mutant himself, leading the forces of Camelot to campaign against all his kin. But, curiously, there's one particular "secret history" Marvel has yet to explore.
Professor Charles Xavier's father Brian worked at what was generally believed to be a nuclear facility at Alamogordo, New Mexico. He died in mysterious circumstances, and his co-worker Kurt Marko - the Juggernaut's father who married his widow - was revealed to know about his step-son Charles' powers, only revealing this after he too was critically injured in a lab accident. In 1992's X-Men #12 by Fabian Nicieza and Art Thibert it's revealed that, as an adult, Charles Xavier learned the dark truth of Alamogordo; it was secretly dedicated to experimenting upon mutants - and it was run by the twisted geneticist Mr. Sinister. This secret was revealed to Xavier by Carter Ryking, a mutant whose father had also worked in the lab with Marko and the elder Xavier. It was through Ryking that Xavier learned his father's work was part of the Black Womb Project established by the U.S. government with still-unclear connections to the Weapon X Project that created Wolverine; Mystique and her wife Destiny were also involved somehow.
Marvel began to build upon this, hinting at a secret mutant war woven through the 20th century - one involving Magneto and, curiously, the X-Men's Banshee. When Emma Frost entered Banshee's mind in 1994's Generation X #10 by Scott Lobdell and Tom Grummett, she learned he had worked alongside Magneto back when Banshee was an Interpol agent, hunting the serial killer destined to become Omega Red. Back then, Magneto seemed dedicated to preventing the genetic war between humanity and mutantkind rather than stoking its fires, and Emma sensed Banshee was tied to Magneto's transformation into a supervillain.
All these hints were largely forgotten until 2008 with Mike Carey's X-Men Legacy run. A master of continuity, Carey picked out the Alamogordo subplot and revealed Sinister had experimented on all the mutant children from that facility, seeking a way to preserve his own consciousness after death. That doesn't seem to have been the limit of the experiments at Alamogordo, though; there were clearly other secrets there. Now, with the mutant race assembled on Krakoa and mutants able to raise the dead - including the now-deceased Carter Ryking - there's no reason the X-Men can't finally learn the truth about this secret mutant war.