X-Men #12 carries on immediately from the end of #11, with Cerebro detecting a massively powerful mutant. Xavier thinks he knows what it is, so explains his life-story, and how his elder step-brother, Cain Marko, became the Juggernaut. Flashback scenes are interspersed with the Juggernaut conducting the first attack on the school, and gradually penetrating its defences.
This is our first significant origin story for any mutant (excluding the panel or two for Wanda in #4), and we see how Xavier was able to read thoughts as a boy, but apparently just assumed it was normal, and only realised it was a special power when he was older, after the death of his step-father. This is very similar to some queer puberty narratives. By his late teens he is self-identifying as a "mutant".
We then get the story of Xavier and Marko serving in the Korean War, and them finding the Temple of Cyttorak, and Marko holding the gem and being transformed into a human Juggernaut. The issue concludes just as Juggernaut confronts the X-Men - making this the first proper two-part story. Issue #13 gives his side of the story, with him claiming that he'd taken all that time to dig himself out from the stone. He gets dumped in a big hole by the X-Men, but is soon able to escape (as he rhetorically asks - "Haven't they realized yet that nothing can hold back the Juggernaut?"). After distracting him for a while and nearly losing, the X-Men remove his protective helmet, allowing him to be stopped by Xavier's mutant brain, amplified by his new "mento-helmet".
X-Men #12 makes the chronology rather complicated. Xavier fought in the Korean War, and we know he'd at least started college before then, and that he's been keeping his head down, so probably won't be attending college too early. So he is at the very youngest 18 in 1953. Which makes his birth year 1935. In our very first issue Xavier says that he was "born of parents who had worked on the first A-bomb project". I joked that this meant the British Tube Alloys project rather than the Manhattan project, but even if we take that seriously, it still doesn't work. Xavier can't have been born to parents who worked on any A-bomb project, and serve in the Korean war, and this is not a problem that the sliding timeline has presented, but a problem that could have been apparent in 1965. We'll see if the material ever gets around to fixing it (perhaps in the early issues of X-Men: Legacy). It could change the war around (which it might do anyway, to avoid Xavier being too old), or it might posit a secret pre-war atomic bomb project.
Johnny Storm of the Fantastic Four has a small guest appearance in the fight, but his memory of the event is wiped by Xavier and he is sent packing. It was a pretty bad fight, so all the X-Men apart from Jean are injured and in bed. She gets to play nurse (on top of getting to cook for the X-Men on the cook's day off in #6). Woo.