When you meet the Brain, he gives you a dropquote full of numbers with the instruction "First, alphabetize all the letters." So you take all the letters in all nine agents' passphrases — there are 107 letters altogether — and alphabetize them. Then you plug in the nth letter of the resulting string for each of the numbers in the dropquote, so 1-9 become A, 10-13 become B, and so on.

Then you just solve the dropquote, and you get:

TO ATTACK PROF MORIARTYS LAIR CALL HQ TELL THEM WHERE IT IS AND SAY GET SNOWED.