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Watson received a note requesting his assistance at the apartment to help treat a dying woman.
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Sherlock made it look like Moriarty wrote the note summoning Watson to the apartment.
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Moriarty must have been in search for Sherlock at that time, which meant he was still safe.
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This means Sherlock didn't leave the falls, which means he and Watson are not too far apart. Sherlock wouldn't leave without his walking stick.
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Sherlock asks a young swiss boy to deliver a few letters for Watson to find. He first takes a letter to a place where Watson will see, that being the place he finds the "goodbye" letter, then delivers another directly to Watson saying he got into a fatal fight with Moriarty.
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Both Moriarty and Sherlock were walking in one direction. The reason no footprints lead back to Watson was that Sherlock did not take the same route back to Watson.
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Watson sees a lot of broken branches and scraped mud indicating a struggle. This could have been the way Sherlock struggles to fight off Moriarty before throwing him off the cliff, or just a set up by Sherlock to add to the "death".
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Moriarty's body must have been sucked into the swirling water below while Sherlock swiftly escaped before anyone could see. He wanted everyone else to think he was dead so he could protect himself, Watson, Lestrade, and Ms Hudson.