Mr. Doodles probably was donated to the Bikini Bottom Animal Shelter- for money, of course. Either that, or he was just largely ignored by the writers.
Mr. Krabs realized that he did not have the financial means to properly care for his dear pet so he brought Mr. Doodles to a shelter where he was adopted by a loving owner and he now enjoys playing in the snail and worm park from "Gary in Love".
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