Many of the X-Men's greatest enemies have become allies in the era of Krakoa, working together to help unite and amplify mutant interests around the world. But there's one powerful villain who remains one of the most dangerous threats to the X-Men in the world.
Cassandra Nova, an alien spirit who is essentially Professor X's evil twin, still stands as one of the greatest lingering threats to mutantkind.
Cassandra Nova is one of the most dangerous figures the X-Men have ever encountered -- and one of the most personal. The opposite number of Charles Xavier, Cassandra should have actually been his twin sister. However, even the unborn Xavier could sense something dangerous about Cassandra and caused an accident that resulted in her apparent stillbirth. Cassandra survived this attempt on her life as a psionic being, slowly rebuilding her body and eventually dedicating herself to destroying her brother and the cause he'd come to so firmly believe in -- peace between mutants and humans. With powerful psionic abilities of her own, Cassandra was a major antagonist after she debuted in Grant Morrison and Frank Quitely's New X-Men #114 in 2001.
Nova was directly responsible for the Sentinel assault on Genosha that resulted in 16 million mutants being murdered. She briefly possessed her brother and even brought chaos to the alien Shi'ar Empire by infecting Lilandra with madness. Eventually, Cassandra was contained within the body of the Imperial Superguardian known as Stuff and was held within the Xavier Institute. She attempted to escape her prison in Astonishing X-Men and actually came close to claiming Shadowcat's body as her own, only to be stopped by the X-Men. However, Nova eventually escaped and resurfaced after the rebirth of Jean Grey, proving herself to be a formidable foe for Jean's efforts to bring peace between humans and mutants.
Nova moved around the world, infecting people with not only her cruel telepathy but with microscopic Sentinites that could place anyone under her control. Nova stirred up anti-mutant hate around the world and set up the governments of the world to attack all mutants everywhere. However, Jean and her team in X-Men: Red were able to stop her plans from succeeding; Jean even used the Sentinites to force Nova to feel empathy for the first time -- bringing the villain to her knees in tears. Jean promised to help Nova grow and become a better person -- only for the chaos of Age of X-Man to take Jean and most of the X-Men briefly into a parallel universe. This means that Cassandra is unaccounted for, which could prove to be very dangerous.
It's possible that Cassandra Nova could be redeemed. Plenty of X-Men are former villains who saw the error of their ways. The future of "Here Comes Tomorrow" even saw a long-living Nova eventually take the name Xavier and become a leader to that time period's X-Men. However, there's a darkness to Cassandra Nova that can't be underestimated. The fact that Jean and the X-Men didn't get the chance to fully help her doesn't bode well either, with the mutant heroes now distracted by their efforts to protect Krakoa and establish it as a major home for all mutants going forward. But that could all be complicated by Nova returning to her old ways and pushing any nations already worried about mutants into outright aggression against Krakoa, let alone stoking the fires of hate in places that already despise mutants.
Considering the way that Krakoa has treated the Scarlet Witch, a proven hero, with scorn for what she's done to mutantkind, Cassandra Nova would almost certainly be considered public enemy number one on the mutant island. Despite her apparent turn, Cassandra's immense psychic powers could easily turn the rest of the Marvel Universe against Krakoa in a violent way. Nova could even see the escalation of Xavier on the world stage as reason enough to meet him halfway. If Cassandra were to return, she could try to repeat what she did on Genosha, and she could bring the rest of the world along with her.