Following her mental breakdown, the Scarlet Witch used her mutant powers in an unprecedented manner: she altered reality to allow mutants to be the dominant species. The resistance movement eventually got through to her, but at a great price. As she restored reality she suppressed the expression of the mutant gene, affecting the vast majority of the existing mutants. The remaining mutants were now a species on the verge of extinction.
This change also affected mutant births. Since "M Day" (the nickname for the day when the mutant population dramatically declined) no new mutant births have been detected. All this changed when a single mutant girl was born in Cooperstown, Alaska. This began a major race to lay claim to the miracle child by the X-Men and other mutant groups. The Purifiers (one of the mutant factions) killed many humans in search of the child. Cable found the child and eventually took her into the future to safeguard her. He named her "Hope Summers".
With triumph comes tragedy. Professor Charles Xavier is accidentally killed by Bishop, a former X-Man. Rather than continue at the Xavier Institute in Westchester, they move to San Francisco. Mayor Sadie Sinclair is openly pro-mutant and accepts them in her city.
Cyclops later learns that Professor X is alive. His life was saved and mind restored by Exodus of the Acolytes. The Acolytes saved Xavier expecting that he would lead them. He rejects their offer and leaves, despite their efforts to keep him there. After a lengthy discussion, Cyclops and Professor X agree that Scott should lead the X-Men as he sees fit.
Simon Trask leads his anti-mutant group "Humanity Now!" to San Francisco, the current haven to all mutants. He is intent on passing legislation that will limit the reproductive rights of all mutants. His rationale is that the last time a mutant was born, it destroyed a town (an exaggeration). He poses the question to the American public: do you want your town to be next?
As he and his followers make their way to city hall they are met by Beast and his delegation from the mutant community. Their intentions are to block the most direct route to city hall and possibly annoy or delay them. Their intentions were admirable. Emotions run high and when Trask suggests to his followers that they're surrounded, the fuse is lit.
Although its never clear who threw the first punch, both sides fight with equal intensity despite Beast's pleas to remain calm. Many of the mutants are caught on tape beating up normal humans. When the police arrive, Beast is tasered and arrested along with other rioters. Trask and his group are sent to St. Francis hospital for medical treatment. Once released Trask calls for a press conference and plays the role of harmless protester to the hilt.
In response to the riots, Norman Osborn arrives and plans to assist in keeping the populace under control. He arrives too late to stop the first wave of violence that occurs throughout the city despite Cyclops and his team's efforts to contain it. The Castro Street Theater is destroyed by a Molotov cocktail from an anti-mutant protester. In other areas mutants are forced to stand against their more radical brethren in the hopes that a less invasive, civil agreement can be reached.
Near San Francisco Bay, Osborn and his Avengers set up shop. Osborn selects specific areas for his team to cover and regain control. His explicit orders are to detain the rioters until they can be arrested. No fatalities. Ms. Marvel (Moonstone) is sent to The Castro area. Spider-Man (Venom III) is sent to Hayes Valley where he engages the X-Man Colossus in a one-on-one fight. Hawkeye (Bullseye) is sent to The Embarcadero where he scares away the protesters while fighting off the urge to kill everyone in sight. Ares is dispatched to City Hall to protect the mayor. Sentry is held back; he's the last option.
At this point Osborn meets with the White Queen. He reminds her that their arrangement through The Cabal was that she would keep the mutant population under control and in exchange, he wouldn't meddle in their affairs. Since she couldn't keep her end of the deal, he will step in. He gives her a dossier detailing his new plan and a new costume to make her his Black Queen.
Osborn later meets with the press to declare San Francisco, Oakland, and Berkeley to be under martial law for the time being. Scott Summers, the self-appointed spokesperson for the mutant community, is considered a person of interest for inciting these riots and will be brought in for questioning. He states that he is not the only one with questions for him and brings out Professor Xavier. Xavier distances himself from the actions of the rioters and pleads with Cyclops to turn himself over to the authorities.
The scene then shifts to the detention cell set aside for Beast. He hears a faint telepathic plea and learns that the real Charles Xavier is in the same facility. The weakened Xavier warns Beast that "they" are trying to take away all mutant powers.
On the surface, this looks like a pointless crossover between Uncanny X-Men and Dark Avengers. However Osborn reminds us of the agreement that he made with the members of his Cabal. Since Frost can't keep the mutants under control, he'll do it. She can't refuse him without Osborn revealing their association.
Scott's hands aren't exactly clean either. He has a new X-Force team that are sanctioned to use lethal force if the situation calls for it. Their respective secrets are creating a rift between them. This could potentially end their relationship.
4 webs. Solid opening chapter to this arc. At times it seems a bit padded, but when you have this many characters to handle, a 1 - 2 sentence explanation doesn't cut it.
The birth of the mutant messiah (Hope Summers) occurred during the Messiah Complex crossover. This started in X-Men: Messiah Complex #1 and proceeded through X-Men (Vol. 1) Uncanny #492-494, X-Factor (Vol. 3) #25-27, New X-Men #44-46, and X-Men #205-207
Simon Trask resurfaced and started anti-mutant groups in X-Men (Vol. 1) Uncanny #505
The Cabal first met in Secret Invasion #8.