The Disaster
Examine the first letter carefully
and you will work them out.
The old professor had been purposefully tricky with his language to throw his readers off the trail. When Tom first read that clue, his mind immediately interpreted it as referring to the very first letter he'd received in the mail from Professor Atticus. And once that had been set in his mind, he'd never even considered the possibility of a different meaning. But what the mysterious man really meant was something entirely different.
The first letter.
Not the first envelope. Not the first paper. Not the first message.
The first letter.
Professor Atticus meant that Tom needed to literally examine the first letter of something. And only one possibility made sense. Even though some of the twelve clues had not seemed like clues at all, Professor Atticus had been very clear.
Everything is a clue.