Variant Rules. Located under the disclaimer. Copy and Pasted below if you can't view the PDF.
Two Player Game
In a two player game, each player chooses a single character.
During setup, Loyalty cards are not dealt out.
At the start of the sleeper phase, create a loyalty deck
consisting of 1x “You are a Cylon” and 2x “Not a Cylon” cards.
Then add a number of “Not a Cylon” cards to the Loyalty deck
equal to the number of resources that are half or lower (red).
Then shuffle this deck, and deal 1 Loyalty card to each player.
Note that the Sharon “Boomer” Valerii character may not be
chosen when playing this variant.
On BoardGameGeek there was a note that if you exclude Boomer from character selection, you may want to exclude Baltar also.