Yuan Shikai and the Manchu Dynasty

When Yuan Shikai returned to Beijing, it was basically as absolute master of the future of the Manchu dynasty. He had no more loyalty for these people than he'd had for the Guan Jue Emperor. And yeah, as you pointed out, they should have cut his head off. They wouldn't be in this situation if they had. It's possible that he feared Japanese intervention. The only, I guess, other alternative was a partition of China along the line of the Yangtze era, like two Chinas,. But nobody on either side wants that.