The Cylons arrange a meeting for the purpose of making a truce but little do the humans know that the Cylons wish to destroy them. By the time they work it out it is to late. Only the Battlestar Galactica survives and Commander Adama gathers up all survivors and leads them away from chaos
The fleet stops on the planet Carillon to pick up supplies and fuel so they can continue on their journey. Adama thinks something is wrong and a newly elected Council member seize power from Adama.
Most of the fleet's population, along with the Viper pilots, relax at the casino on Carillon. Adama thinks that the Cylons are using Carillon as a trap and suspects an imminent attack but none of the council members believe him.
Starbuck and Apollo when on patrol discover a huge void in space. Adama wishes to go through it as he remembers in an ancient book it says it is on the way to earth. Boomer discovers a Cylon listening post on an asteroid and when he and Jolly return they are both dizzy, Boomer skips decontamination to go to Apollo's bachelor's send-off party and end up making all the pilots sick.
Adama continues to lead the rag-tag rebel fleet towards the planet Kobol where he hopes to find clues on how to reach earth. Starbuck is captured by the Cylons in order to force a truce plot by Baltar who is now working for the Cylon's.
Apollo's ship is damaged and he is forced to land on a Baron farming planet. A young boy finds him and he is then taken to a farm house where he spends the next few days with the boy and his mother. Apollo soon learns that there is a lost Cylon working for a man and must find a way to destroy him so that he will stop causing problems with the other farmers.
The team on the Galactica build a new ultra fast but unarmed Viper to do long recon. Starbuck volunteers to take the mission. He runs into a ship being chased by another and intervenes. Starbuck is caught by galactic police and is imprisoned on a prison planet and must find a way to escape.
While on a patrol, Viper pilots notice a giant pulsar cannon at a Cylon outpost. Adama realizes that Baltar is trying to lure the Galactica into a trap, so Adama sends a team of commandos down to the planet to destroy it. What the team leaders aren't happy about is that several of the team are violent prisoners.
The team of commandos which include several prisoners land on the planet in order to destroy the cannon. The get help from a group of people that serve the Cylon's in order to help destroy. They realize that a human is helping the Cylon's by making technology for them. The team manages to get his help in order to destroy the gun.
After a Cylon attack much of the fleets food supply was destroyed so they must find a planet in which to trade. They land on a farming planet which is plagued by small pig like animals called Borays. Will the team be able to overcome the Borays and get the food they need.
When Starbuck crash lands on the planet Atilla, where the Cylon's have destroyed all humans except for several children. The children hunt the Cylon's as warriors in order to free their father who the Cylon's hold in their fort. With the help of Starbuck will they be able to free him?
On a patrol Starbuck and Apollo are amazed to discover that the Battlestar Pegasus which they assumed was destroyed. The Pegasus is commanded by Commander Cain who is a living legend for many people in the fleet.
The commander of the Pegasus, Commander Cain makes the Galactica join in on a full out attack against the Cylons. Adama is unsure about it because he believes the plan to be a suicide mission and will destroy the lives of the entire fleet.
After a Cylon kamikaze attack on the Galactica, it is burning in space. Their is no way to extinguish the fire that has already killed many and has left Boomer, Athena, Boxey and many others trapped in the rec room. The only way to free them is via a dangerous spacewalk by Apollo and Starbuck.
The fleet is attacked by glowing lights, which are traveling past them much faster than they can follow. Apollo, Starbuck and Sheba find the remains of a spaceship. They find a man named Count Iblis at the wreck and he helps them capture Baltar.
Count Iblis continues to gain popularity with the Council for delivering Baltar to them. Adama continues to think there is more to him that what he is telling them. Apollo, Starbuck and Sheba return to the planet and investigate the crashed ship.
Starbuck meets an old man who is a con artist called Chameleon who convinces Starbuck that he is his father. Apollo soon learns that he is not telling the truth but only using Starbuck to avoid a trio of bloodthirsty Borellians who want him dead.
After a popular sporting event one of the members in the team Starbuck was playing and his main rival is found dead. Starbuck is the main suspect and Apollo is the only one who believes him and must prove his is innocent.
While on patrol Apollo and Starbuck find a primitive ships carrying a family of a man, woman and 4 children. Speculation soon spread around the fleet that the mysterious people they have found are from Earth but is that who they really are?
Starbuck, Apollo and Sheba take the people from the sleeper ship to the planet they were heading, a farming planet. Once they arrive they find themselves with a new threat called the Eastern Alliance, a Nazi like society who is intent on destroying them.
Baltar, with the help of fellow prisoners, organizes a takeover of the prison barge with the idea of fleeing the Galactica and taking personal revenge in the process.
Apollo has a routine patrol interrupted and finds himself on a strange world where he is treated as if he is an entirely different person. Even as he wonders whether this world is the Earth the fleet has been searching for, Apollo tries to stop an all out war between rival factions that would destroy much of the population.
After a lengthy time, the Cylons are back with a basestar that looks to block the Galactica's path. Tired of running, Adama decides to go on the offensive and concocts a plan to attack and destroy the looming Cylon menace.