On an episode of the "Breaking Bad Insider Podcast," hosted by "Breaking Bad" editor Kelley Dixon and Gilligan himself, the showrunner admitted that he pitched a storyline in which Skyler died a horrific death.
"You did pitch a pretty crazy thing with Skyler," Dixon said. "You told us she was going to kill herself." Gilligan said one of his ideas was that Skyler would leave with Walt, and they would be "holed up in some Motel 6 or some place." While his wife was in the bathroom, Walt would tell Skyler that it was going to be alright and that, in typical Walt fashion, he had a plan. He would continuously call her name until he "finally forces the door open and she's in a bloody tub or something like that, opened up her wrists. It was very dark."
Gilligan said he was leaning toward using the idea, but the other writers thought it was a "bridge too far" and "unnecessary." For a show as dark as "Breaking Bad" already was and considering that we already saw Skyler nearly drown herself in her swimming pool earlier in the show, an actual suicide might have been too much to handle for any viewer.
Instead, the last we see of Skyler in the show is of her holding a cigarette and Walt finally admitting to her that he did all of his heinous crimes not for his family, but for himself. "I liked it. I was good at it," Walt tells her. She lets him see their daughter Holly one more time before he leaves to save Jesse from a neo-Nazi compound with the help of a mounted machine gun in his trunk.