At the start of each episode, host Anderson Cooper encouraged viewers to keep an eye out for a hidden clue to the Mole's identity. One clue was revealed in each episode, ranging from straight-forward references to Bill's background to highly esoteric wordplays. Some clues were presented to the players, while others were available only to the home audience
Episode 1: All outdoor shots of the night sky were absent of stars, save for one. This shot, taken outside the cabin where the players stayed shortly before the Burn Bags Burn game, featured a digitally-enhanced sky showing the constellation Pisces, the sign of the Zodiac under which Bill was born. Astute viewers could have used Bill's biographical information on the ABC website to deduce this.
Episode 2: In the opening montage to the episode's execution, two pictures of Zodiac signs are shown. The first is Virgo, which was the sign of that night's victim, Ali. The second sign shown once again is Pisces.
Episode 3: A journal written ostensibly by the Mole was planted for the players to discover and read. In it, the Mole explains how eliminating his first victim, Bob, was "too easy", as he had spent all of his time "schmoozing the ladies". This should have ruled out any female from further suspicion.
Episode 4: Upon arriving in Italy, the players are welcomed with a telegram sent by "La Talpa", which is Italian for "The Mole". The telephone number given at the bottom was 0024-5500, which was clearly not a valid number (as dialing 0 in most countries will connect you with an operator). Instead, by using the letters associated with numbers on a phone keypad (starting with 2 as A, B, and C), the numbers spell out Bill's name. In fact, the numbers preceding the telephone number were 843-885347, which when combined with the telephone number spell out "THE MOLE IS BILL".
Episode 5: At the conclusion of the Think or Sink game, Anderson talks about how many believe that William Shakespeare was a "scoundrel" for plagiarizing the story of Romeo and Juliet from a local playwright. (The Italian translation of the play's title, "Giulietta y Romeo", served as the solution to the game.) Anderson's story about Shakespeare was intended to subtlety point out that the William in their midst was also a scoundrel.
Episode 6: When the bike-riding teams in the Wine Delivery game reached the midway point of the course, Anderson would hand the rider a bottle of wine from the Lamole vineyard, while eating an apple in both instances. The apple was a reference to the official symbol of Bill's home state, Washington.
Episode 7: One of the more obvious clues given to the players, prior to execution they were each instructed to rank their fellow players in order from favorite to least favorite on a dollar bill. This was intended as a clear reference to the name of the Mole, Bill.
Episode 8: The only time a painting was ever in the frame while the players took the execution quiz was in this episode, where a portrait of a large schooner was prominently shown on the wall - a reference to Bill's background as a Navy admiral.
Episode 9: During the Matrix-like grid of letters that flashed on the screen during the opening title sequence, the word "AdMiRaL" is displayed in the top-left corner for a split-second. Once more, another reference to Bill's background as a Navy admiral.
Episode 10: When the Morality Game takes place while the men in the group tried unsuccessfully to peddle their wares, a local man visits the men's table and leaves behind a book which contained the lost money. The book was Romeo and Juliet - an obvious reference to the clue made in Episode 5. Both Al and Bribs noticed the coincidence, but neither made the correct connection from it.
Episode 11: Two clues were provided during this episode. First, a montage of three model ships were shown just prior to the remaining players entering Anderson's Fun House - once again alluding to Bill's naval career. Second, the players are treated to a dinner consisting entirely of food from McDonald's. Anderson mentions at the end of the meal that the execution is approaching, meaning that one player has just had their last supper with the group, "courtesy of 'Mickey D's'". Mickey D's is a nickname for the fast food franchise, but it also serves as a clue to Bill's last name, McDaniel.
Episode 12: Much like the clue in Episode 9, a message is concealed among the letter grid in the opening title. This time, however, the message is far more blatant, as "Bill is the Mole" is spelled out along the top of the screen.
