Ironically, I'm sure the huge bureaucratic shuffle is less trouble than literally wresting the existing structure from Haruhi's hands. Done well enough, she'd never even notice that what she has left to command is just a shell bureaucracy, little more than a handful of paper pushers.
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"You know how parents tell you everything's going to fine, but you know they're lying to make you feel better? Everything's going to be fine." - The Doctor
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"You know how parents tell you everything's going to fine, but you know they're lying to make you feel better? Everything's going to be fine." - The Doctor