What will Lisa Murkowski do in 2016?

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Option 3.

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I'm honestly not sure. She recently sent a Cease-and-Desist letter to Begich's campaign for repeatedly including her in his campaign ads, and she's promised to campaign hard for whichevever Republican (save Miller) is the nominee. She's made it clear she wants a Republican colleague.

That, and like Miles said, she could have the Energy gavel.

It will be interesting to see what she does do. Her approval isn't great with Republicans, but I think she has time to improve on that, and her campaigning against Begich could be a sign she's thinking about this.

Yeah, the problem is it's a big risk. After all, if she lost a primary when her approval was very high amongst Republicans, it wouldn't be too hard to see her losing one now that she's in the negative with them. Alaska also has closed primaries, meaning she couldn't pull a Cochran and rely on Democratic crossovers. It could also depend on whether or not she has a legitimate challenger or just Miller-esque ones (or even possibly Miller himself). It will certainly be interesting.

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Option 1. I don't see her running as a Independent unless she loses the Republican primary.

But can't she not do that if she loses the primary, and that's the entire reason she had to do a write-in candidacy last time? Unless she wants to go back to being a write-in candidate, which would be quite entertaining but probably wouldn't work again considering whichever Republican beats her will (presumably) be more competent than Joe Miller.