Let me preface this by saying that I didn't really enjoy Avengers Disassembled due to its execution, but I really like the idea of the Scarlet Witch being behind it all. It all makes a lot of sense now.
Taken over a long time, Wanda is and always has been damaged goods. Her family-- Magneto, Quicksilver, and herself-- is quite obviously mentally ill, suffering from some type of bipolar disorder that had manifested itself over trauma related to abandonment. (There are often genetic roots for depression and other sorts of emotional disorders.) It's most clear, I think, in Magneto: his family was taken from him by the Nazis, and he has taken mutant kind as a surrogate family he must protect while avoiding intimacy with his true family, Pietro and Wanda. His actions are often erratic; one minute he seeks to punish humanity for their crimes, other times he seeks conciliation.
Quicksilver has also gone off the deep end in the past. The reason? An insular, distrustful person by nature, Pietro found love in the arms of Crystal, who is a member of an insular, distrustful culture, although she is relatively well adjusted. The Inhumans never accepted him, however, seeing him as valorous, but still genetically inferior. When Crystal betrayed him by sleeping with another man-- a normal human at that-- he lost his mind, battling the Avengers and the FF. Eventually, he teamed up with fellow mutants in X-Factor, but even that was a means to an end. He never felt "comfortable" with himself until he a) led the Knights of Wundagore, a surrogate family of man-animals which reminded him of his youth being raised by Bova, his true mother figure, and b) reunited with Crystal, thereby reconnecting with the only familial bond that gave him stability. Except for, of course, his sister.
Wanda's always put on a brave face, but let's face it: she's been doomed from the beginning. Abandoned by her true father, her mother died in childbirth in the midst of a supernatural battle against Chton, the source of all black magic in the Marvel Universe. During the birth, Wanda has struck by stray bolt of mystical energy, which altered her latent mutant powers into "hex" bolts and, later, so-called "chaos magic". (The link to dark powers/evil was there from the very beginning; it just never really worked through until recently. I'll get to that later.) Bova gave Wanda and Pietro to the Maximoffs, who abandoned them when Wanda's powers began to manifest. They were rescued from an angry mob by Magneto, who allegedly was unaware that he was their father, but just happened to be looking for new recruits in Transia, where he had lived with Magda. In Magneto, Wanda had her first surrogate father figure, although, ironically, it was her true father. He did not treat her well, ignoring her for the most part while truly repulsive men like the Toad (laughably) and Mastermind (more sinisterly) drooled over her. It was Pietro who protected her.
Eventually, Wanda and Pietro join the Avengers, where Wanda meets her second father figure, Captain America. She's attracted to Cap, but let's face it: he's as unattainable as it gets. But he's still the perfect man in that he protects her as only Pietro has in the past. Hawkeye is there as well, but he does not have the same shine to him. (I mean, Hawk's my favorite Avenger, but he's still a guy that's going to say anything to get into a woman's pants. He's the Everyman Avenger!) True love hits Wanda in the form of the Vision, a man who isn't a man at all, just as Wanda isn't really human. I speculate that Wanda's dark magic works via her subconcious to influence events in order to give the Vision feelings for her. Once the cap's off the bottle, the magic flows more easily. Vision and Wanda marry, but Vizh is unable to reproduce. Wanda taps into her dark power to create children. These children are apparently aspects of Mephisto's power, and he sends Master Pandemonium to get them back. Mephisto absorbs the children back into himself around the same time when Vision is disassembled. He is rebuilt with no emotions. Wanda has been abandoned again, and she goes off the deep end, becoming a Dark Scarlet Witch. The dark aspect of herself gains control because of this trauma. She is restored to herself due to the intervention of the her friends in the WCA, particularly Wonder Man, who is, after all, the pattern for Vision's personality. She compartmentalizes her pain as abuse victims often do as repressed memories.
Now, here's where it gets really interesting: Wanda is used as a magical tool by Morgan Le Fey, the mythological sorceress who was originally responsible for Chton being trapped between dimensions under Wundagore. Morgan sets up an elaborate scheme to distract the Avengers with Asgardian menaces, while her true prize is Wanda whose power will help her tap into Surtur's sword to warp reality. Morgan, I speculate, understands the true nature of Wanda's power-- that she is a purer link to Chton's power that even the Darkhold. Wanda and, to a lesser extent, the Avengers defeat Morgan by summoning Wonder Man back from the void. Suddenly, Wanda can summon Wondy back anytime she wants. He feels that it is their love for one another that brings him back, but she is not sure. Eventually, she goes to Agatha Harkness in the midst of a battle with the Grim Reaper and several deceased Avengers. She is convinced that the Grim Reaper is the one who has controlled Wondy's comings and goings, but Agatha, herself a link to dark power, tells her that the answers are within herself and explains the true nature of Wanda's power to her.
Of course, Agatha Harkness is dead. This is the dark force within Wanda asserting itself. Eventually, it works through Wanda's repressed memories until Wanda, already prone to mental illness, snaps. And then she lashes out at the one constant in her life: her surrogate family, Avengers, who let her down at her lowest moment, just as she has always been let down by family.
But why now?
In JLA/Avengers, two key things happen to Wanda: 1) she experiences the true sensation of pure, defined "chaos magic" and how powerful it can be; and 2) she sees glimpses of what had been within the Gamesmaster's screen, rediscovers her pain, and realizes how malleable reality is to someone with power. Like the rest, she conciously forgets when the two universes "right" themselves, but things are already working within Wanda's dark subconcious. This only reinforces them.
It begins with Wanda subconciously reaching out to her ideal man, Captain America, to save her with his love. (In Captain America and the Falcoln) But that doesn't work. So, she snaps, the dark powers act out through and towards characters who either resemble or are responsible for her state of mind:
--Jack Hart, whose problems and eventual death were caused by the negligence of his father.
--Scott Lang, who in death abandons a young daughter, just as Wanda was abandoned.
--She-Hulk, who, like Wanda, has a dark, uncontrollable aspect to herself.
--Iron Man, who betrayed her during the Crossing when she was leader of Force Works and through his alcoholism and womanizing, represents the weakness of men in general.
--Vision, her former husband reduced to what he was when the Avengers first encountered him, a trap set by Ultron.
--The Kree, another race of being superior to humanity, much like her true father feels mutants are.
And in the end, who comes back to save her? Her father, the man who was never there for her.
Of course, I could just be full of crap.
, but it made me sign on to the site, finally, to give praise...as hurtful as it looks, all of it is soooo true 
