X-Men #4 (1964, March)
This issue sees the return of Magneto, and the debut of his Brotherhood of Evil Mutants. Which seems like a bit too on-the-nose a name for him to pick out himself, but I guess he was feeling dramatic that day. Anyway, by Lee, Kirby, Reinman and Simek, “The Brotherhood of Evil Mutants!”

These guys need better PR. And yes, the Scarlet Witch is wearing green.
It starts with the X-Men celebrating their one-year anniversary since the school opened. They have cake! Which Scott shoots with his eyes!
It then switches over to the Brotherhood eating a meal. Toad’s a pig, Mastermind’s an arrogant ass, Scarlet Witch is stuck-up, and Quicksilver’s whipped. Magneto steals an old ship, and we find out that Quicksilver and Scarlet Witch only serve him because she owes him her life. So the attractive mutants aren’t evil, after all, so that’s a relief. Whew.
But then Magneto says something important. He says that humans hate and fear mutants. Ah, the theme arises. Of course, Magneto’s only saying it to convince Quicksilver and the Scarlet Witch that conquering humanity is fine. But still, it’s the first mention of the idea that humans hate and fear mutants, so it’s significant.
Anyway, the Brotherhood takes over the country of Santo Marco, a South American nation. Whose people look like this:
So the X-Men go down to beat him up. He senses them when they get there. He feels them in his brain!
Only in comics can you get a moment like that. Where a character rants that his enemies are there, and he can feel them in his brain! “I feel them in my brain!” And he’s not just paranoid and delusional, he’s right. Comics! Also, Angel gets captured again:
Lots of fighting, everyone on both sides gets to show a little of what they can do, Magneto decides to nuke Santo Marco to take out the X-Men, and Xavier gets hurt by a bomb and loses his powers. Oh no!
The series is really starting to come together well at this point. The addition of the Brotherhood of Evil Mutants provides a very interesting set of recurring villains, who function as a dark reflection of the X-Men. Quicksilver and the Scarlet Witch serve as sympathetic antagonists, making the fights more complex. The personalities of the X-Men themselves are pretty well-defined by now. And Xavier’s injury at the end raises the stakes a little, and gives a sense that they’re facing real danger.