probably the brotherhood
He means the mechanist/AntAgonizer quest.
Either you defeat the Mechanist, or the AntAgonizer, or you convince one of them that the other is dead, or that one of them should stop, or you get them to both stop, or you can kill them both.
We could assume that at the very least the Mechanist doesn't die, but I don't think that's necessarily true.
Even if the Mechanist were left alive, and still acting like a superhero, then it's 10 years later, and he's in his 50's. A bit old for an inexperienced guy to be trekking between the Capital Wasteland and the Commonwealth, surely.
If the Mechanist makes a full re-appearance, I reckon it will be a descendant of his, or possibly an entirely different person, who may even be from the Commonwealth.
After all, the Mechanist is a comic book character, and there are plenty of comic books, and even costumes in the Commonwealth.
He's also described as an enemy of the Silver Shroud, so there might be some unique dialogues if you meet him dressed as the Shroud, or wear his costume to meet Kent Connolly.
Poll