There are three different scenarios that may be played: the original scenario following humanity's journey to the planet of Kobol, the Pegasus expansion scenario following the fleet to New Caprica and the escape from the planet that followed, and the Exodus expansion scenario following humanity's travel to and departure from the Ionian Nebula.
- Human Victory: Kobol scenario: Reach Kobol by making one final jump after accumulating a Destination Score of 8 or more (Every time you jump you will earn a Destination Card with a score between 1 and 3), OR New Caprica scenario: Jump the fleet to New Caprica by accumulating a Destination Score of 7 or more, then subsequently jump the fleet away from New Caprica while maintaining at least one of each resource (Fuel, Food, Morale, Population) (See dedicated rules section for the New Caprica phase of the game.), OR Ionian Nebula scenario: Reach the Ionian Nebula by accumulating a Destination Score of 8 or more, then making one final jump. (See dedicated rules section for the Ionian Nebula scenario.)
- Cylon Victory: End humanity. This is done by destroying Galactica (damage six locations), dropping one of the fleet's resource stats to 0, or getting a Centurion Boarding Party far enough into Galactica's innards.
- Cylon Leader/Sympathetic Cylon Victory: Fulfill the conditions stated on their hidden Agenda Card – these include allowing either the cylons or the humans to win the game alongside other requirements.
At the start of the game, each player (with the exception of Cylon Leaders) is given one Loyalty Card (Exception: Gaius Baltar, who receives two) that indicates whether or not a player starts out as a Human or a Cylon player. Players take turns in sequence, encountering crises and jumping the fleet towards the destination of Kobol or New Caprica. When a distance of 4 or greater has been reached, the Sleeper Agent Phase activates: each player, including Revealed Cylons, is dealt one more Loyalty Card (Exception: Sharon Valerii, who receives two) that may change that player's alignment. The total number of Cylons present in the game is fixed and dependent on the number of players in the game. It should be noted that with the Exodus expansion, the Loyalty deck will contain one more card than necessary for use with the new execution rules and new loyalty cards.
Certain "You Are Not A Cylon" cards have special designations as being a "Personal Goal" or as "The Final Five". "Personal Goal" Loyalty cards contain conditions that must be fulfilled by the owning players. While these goals may often be detrimental in nature, failure to fulfill the card objectives will result in the loss of resources at the end of the game. "The Final Five" Loyalty cards contain negative effects that trigger when the card is examined by a player other than its controller. There are increased penalties if the card is revealed as part of an execution result.
Instead of a loyalty card, Cylon Leaders start the game with an Agenda card that provides a special win condition. While the Cylon Leader may win with either the humans or the Cylons depending on the drawn Agenda, each Agenda requires an extra condition to be satisfied in order for the Cylon Leader to declare victory. In a 4- or 6-player game, the Cylon Leader draws an Agenda from the Sympathetic Agenda deck, which is more likely, but not necessarily, to be favorable to the humans. In a 5- or 7-player game, the Cylon Leader draws from the Hostile Agenda deck, which is more likely to be unfavorable to the humans.
Sympathetic Cylon Leader Agendas
(4- and 6-player games)
Hostile Cylon Leader Agendas
- Convert the Infidels - The humans have won AND All resources are at 3 or lower.
- Guide Them to Destiny - The humans have won AND Population and morale values are within 2 of each other.
- Join the Colonials - The humans have won AND you are Infiltrating and not in the “Brig” or “Detention”.
- Prove their Worth - The humans have won AND at least 5 Raptors/Vipers are damaged or destroyed.
- Illusion of Hope – The Cylons have won AND 6 or more units of distance have been travelled.
- Salvage their Equipment – The Cylons have won AND 2 or fewer Galactica locations are damaged.
(5- and 7-player games)
- Genocide – The Cylons have won AND Both food and population are at 2 or less.
- Reduce Them to Ruins – The Cylons have won AND 4 or more Galactica and/or Pegasus locations are damaged and Morale is at 3 or lower.
- Show Their True Nature – The Cylons have won AND Either you are in the “Brig” or “Detention”, or you have been executed at least once.
- Siege Warfare – The Cylons have won AND Every resource is at half or lower (in the red).
- Grant Mercy – The humans have won AND Population, morale, or food is 2 or lower.
- Mutual Annihilation – The humans have won AND You have played a Super Crisis Card.
A Sympathetic Cylon may be introduced to the game at the Sleeper Phase in 4- and 6-player games that do not have a Cylon Leader. Sympathetic Cylons draw an Agenda from the Sympathetic Agenda deck, changing their win condition from the normal Human or Cylon condition to that on their drawn card.