@Cabbage, solve all of the Unown puzzles. Once you do, the very first Unown you encounter will have the same first letter as the next Pokemon you will capture. If more than one Pokemon begin with this letter, the next Unown will spell the second letter, and the third, etc, until you only spell out one Pokemon's name. If no Pokemon begin with that letter, or that Pokemon isn't available to you (or such a Pokemon violates any rules), repeat the process until you get a valid result. If you spell out a fully evolved Pokemon, you may capture it's pre-evolution instead if you wish.
IE: You encounter an "A" Unown, and a bunch of Pokemon begin with A. The next Unknown you encounter is a "Z" Unown. That spells out "AZ". The only Pokemon that begin with "AZ" in the Johto Pokedex is an Azumarill, therefore you get to have a Marill or Azumarill.
IE: You encounter a series of Unown that spell out Mew. Since neither Mew or Mewtwo are capturable in Crystal (and plus they're legendaries, they can't be used in a Scramble anyway), you discard the W and try again with "ME".