The first mission of the recently formed uncanny X-Men brought them into direct conflict with Xavier's old friend, Magnus, now rebranded as Magneto, the self-proclaimed "Master of Magnetism." The battle occurred at Cape Citadel, a military base Magneto had taken control of, marking the beginning of a brutal war between the two old friends. In the years to come, Magneto would become the X-Men's most frequent and formidable adversary. The villain was driven off by the young mutants, who were successful in liberating the base from his clutches. Despite the X-Men's heroic actions, their reputation suffered due to growing anti-mutant sentiment.[13]
In their subsequent mission, with assistance from Duncan, the X-Men protected Washington, D.C., against the mutant teleporting thief known as the Vanisher.[141] During their journey, they also discovered that not all mutants were interested in joining their mission when the immovable Blobrejected an invitation into their ranks.[142]Simultaneously, the X-Men found themselves entangled with the broader superhero community: clashing with Iron Man,[143] aiding the Sentryagainst the General,[144] and having a conflict with the Fantastic Four when Professor X fell under the control of the Puppet Master.[145] These and other encounters marked the beginning of the X-Men's many adventures as they navigated the superhero world.
Magneto resurfaced to plague the X-Men, forming his own group called the Brotherhood of Evil Mutants. The terrorist team consisted of Quicksilver, the Scarlet Witch, Toad, and Mastermind. They first confronted the X-Men when conquering the nation of Santo Marco, which Magneto attempted to colonize, but met defeat.[146] Subsequently, the Brotherhood escalated the animosity between the two groups of mutants with a full-on attempt to capture the X-Men, with no success.[147] This was followed by several failed attempts by the Brotherhood to recruit other powerful individuals to their cause, including Namor, the Sub-Mariner,[148] the Blob,[133] and the thunder god Thor.[149] Ultimately, the X-Men witnessed the end of the Brotherhood of Evil Mutants during an encounter with the powerful alien being known as the Stranger, who kidnapped Magneto and the Toad for study and turned Mastermind into stone, neutralizing their threat.[150]
After their graduation,[133] the X-Men were torn apart by the rise of alarming and fanatical anti-movement hysteria.[122] As the group faced these struggles, a future version of Beast happened upon the young students to transport them to the future in hopes of inspiring the decadent mutant society.[151] The time-displaced X-Men spent a long period of time in the future, eventually returning with their memories of this experience blocked. Upon their return, they resumed their adventures,[152] such as fighting Unus the Untouchable.[122] Afterwards, Professor X left Cyclops in charge of the school to thwart the alien Lucifer from conquering the world, a plot foiled thanks to the assistance of the X-Men and the Avengers, sparking the long-standing association and rivalry between the two superhero teams.[153]Amidst these adventures, the X-Men also found a valuable ally in Ka-Zar at the South Pole, where they investigated the hidden tropical paradise called the Savage Land.[154] Furthermore, a dangerous threat emerged in the form of Professor X's stepbrother, Cain Marko, who wielded mystical powers as the unstoppable Juggernaut,[155] but was defeated by the X-Men with the aid of the Human Torch.[156]