Neo. The Only. The One.
THE ONE
The sequel would take place sometime after X: Genesis. This would begin telling Magneto's story as he has flashbacks to his childhood, his life with Wanda, and being estranged from his children. His flashbacks occur as he is leading his Brotherhood and Acolytes in a battle against the Professor X's X Men. It would be the Brotherhood (Sabertooth, Mystique, Juggernaut, and Avalanche) and the Acolytes (Amelia, Exodus, and Gambit) against the X Men (Cyclops, Jean Grey, Iceman, Angel, Beast, Psylocke, and Colossus). This battle does not end well for the X Men as members are severely injured. Professor X attempts to reason with Magneto after the battle, but he is set on destroying humanity whom he blames for crimes against mutants and more importantly what they had done to he and his family. Juggernaut belittles the Professor whom Professor X recognizes as his step brother Cain. He charges at the Professor, but is stopped as Jean shields the Professor with her powers. Psylocke uses her psychic blade to remove Juggernauts helmet and he is stunned by the Professor. Magneto and his forces leave Cain and the injured X Men as he wages war against humans. Fearing there isn't much time left before Magneto wipes out the entire human race, the Professor feels he must summon a second team of X Men to stop Magneto at all costs.
The Professor is also hurt by the fact that Amelia has joined Magneto's cause and feels she is a hypocrite for doing so. He reaches out to her telepathically, but she rejects him.
Professor X uses Cerebro to track more mutants. Once he has found his chosen, he and Jean embark on a mission to assemble this second line of defense. They travel to Canada and find Wolverine, who is instantly drawn to Jean. They then find themselves in Cairo where they recruit Storm. Rogue, Colossus, and Nightcrawler round out the second band of X Men. They all come with their own internal scars that the Professor helps heal while they vigorously train for battle.
Meanwhile, Magneto and his forces are kept at bay by Sentinels. While the sentinels prove to be no match for the master of magnetism, Bolivar Trask and a mysterious geneticist have extracted genetic material from mutants to create super sentinels.
Professor X also finds two more mutants just in case all else fails. Since Magneto played dirty recruiting his step brother Cain and former lover Amelia, Professor X has some tricks up his sleeve as well.
The mysterious figure has taken a special interest in Jean Grey and Cyclops. While the Professor was away recuting mutants, the mysterious figure kidnaps an injured Cyclops.
The Professor arrives back at the mansion and notices something sinister has taken place. He senses that Cyclops has been taken by a threat far greater than Magneto, but must first focus on stopping Magneto.
The Professor sends his X Men (Jean, Rogue, Storm, Colossus, Psylocke, Nightcrawler and Wolverine) into battle with Magneto and his forces yet again. This time they are met by super sentinels. They prove to be formidable opponents, but are no match against the X Men.
The X Men face off against Magneto's forces. Mystique is distracted at the sight of Rogue and Nightcrawler. Both are angry with her for abandoning them.
Wolverine faces off against Sabertooth. Storm and Jean face off against Exodus. Jean starts feeling her powers growing stronger.
Psylocke faces off against Amelia
Colossus faces off against Gambit.
Professor X confronts Magneto and asks him is this the type of world he would want for his children? Magneto asks "what children, humanity took everything from me". "Not everything father" utters a small voice as Scarlet Witch and Quicksilver come into view. Magneto sheds tears as he is reunited with his children. He calls off the battle, which his forces were already losing to the X Men. As everyone retreats, huge blast occurs rendering everyone unconscious and scattered across the field. When everyone awakes several mutants are noticeably missing: Jean Grey, Exodus, Mystique, and Storm.
The missing mutants have been telephoned to a pyramid. Out of the shadows, the mysterious figure is revealed to be Mr. Sinister. He has Cyclops and Jean unconscious inside of a chamber. Mystique, Exodus, and Storm are mounted on horses. Mr. Sinister utters "your horsemen are ready. The apocalypse is at hand".
The ending with Magneto about to destroy everything and then his children whispering "father" and the battle is over sounds kinda Martha-ish to me