It seems to me that Gandalf was sort of handing over his guardianship of the Shire to Tom Bombadil. I mean, he had no reason to keep guarding it. He stayed to keep a watch over the Bagginses, especially Bilbo, and later Frodo, because they had a Ring of Power. When Frodo left with the Ring, Gandalf was with him, guarding what he had originally wanted to guard. Now that Sauron was defeated, and evil vanquished for a long time, the Shire didn't need to be guarded. Aragorn would keep a watch over his northern borders, and the Rangers were still roaming about. The Shire had plenty of protection, and Gandalf knew that Tom would be around for a looong time, so he asked him to keep an eye on the Shire for him.
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But Melkor also was there, and he came to the house of Fëanor, and there he slew Finwë King of the Noldor before his doors, and spilled the first blood in the Blessed Realm; for Finwë alone had not fled from the horror of the Dark.
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