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When the Treaty was being formulated, it was noted by an observer that the Prussian king was pacing on the bank of the Neman river; Napoleon had to "but raise his hand, and Prussia would cease to exist." (McKay)
Suppose that Napoleon had completely ended Prussia as a state at the Treaty of Tilsit by partitioning it, after all he had the Prussians defeated and laying prostrate before him and he could basically do to them what he wanted. Perhaps more land is given to Poland and East Prussia is given to Russia to keep them quiet about the Duchy of Warsaw. Pomerania might be given to Sweden to convince them to join the Continental System and Silesia could be returned to Austria who only lost it relatively recent in the Silesian Wars in the 1740s which would only leave a Brandenburg rump kingdom while making Russia and Austria perhaps a bit more cooperative. The Kingdom of Westphalia, France's puppet, would also probably become the dominant German state and Napoleon can therefore control the German states through Westphalia.
I don't know if this is plausible, but I don't see how the Prussians could stop Napoleon if he had wanted to partition it. Is it plausible? If so, what are the effects?