Air, Parts 1 & 2 A soldier leads evacuees through a stargate onto an unknown, but somewhat familiar, spacecraft.
Air, Part 3 A search team combs a desert planet for a vital mineral to scrub away the carbon dioxide that's accumulating on the Destiny. Meanwhile, Chloe reaches out to her mother via the communication stones.
Darkness When the Destiny's power reserves drop to a critical level, the crew is ordered to use power for essential services only, but the rationing isn't enough to keep Rush from announcing that all on board will die within days.
Light With the Destiny on a collision course with a star, the crew considers abandoning the ship. A grim lottery is held to choose 17 passengers to escape in the Destiny's only working shuttle.
Water The ship's water supply dwindles, prompting Col. Young and Lt. Scott to visit a frozen planet in search of drinkable samples. Meanwhile, the crew attempts to snare an intruder.
Earth General O'Neill wants Col. Young to implement a high-risk plan hatched by IOA scientists that could possibly return the Destiny crew to Earth. Elsewhere, Eli and Chloe use the communication stones to visit their loved ones, culminating in a trip to a club.
Time An away team finds a kino beside a Stargate on a jungle world, which contains video footage of the team that was shot prior to their arrival. Then, an illness cripples the team, forcing them to quarantine themselves on the planet.
Life Lt. Scott and Camille return to Earth via the communication stones to spend time with those they left behind. On the Destiny, the crew explores new sections of the ship, which yields the discovery of a promising Ancient device.
Justice Everyone is shocked when a member of the crew is found dead from a gunshot wound. While at first glance it appears to be suicide, the gun is nowhere to be found. The crew is confined to quarters while a search is performed and when the gun shows up in Col. Young's quarters, he becomes the number one suspect. Fearing a mob scene, Young agrees to a trial and cedes command to Camile Wray. Dr. Rush convinces Wray to give him control of the science team and carte blanche with the new Ancient interface, previously kept under guard. But before Rush can unlock its secret, or Young's trial can conclude, both are needed to explore a planet hiding a secret that threatens the Destiny and her crew.
Space A snafu with the communications stones lands Col. Young's consciousness in an unknown being, resulting in a standoff between the Destiny and an alien vessel and the abduction of Chloe.
Divided Dr. Nicholas Rush and Chloe suffer nightmares following their ordeal on the alien vessel, and Rush suspects that a tracking device may have been placed on the ship's hull. Later, a splinter group on Destiny executes a coup with life-threatening consequences.
Faith Destiny stops near an uncharted star orbited by one planet, this time without activating the countdown clock. Lt. Scott leads a small team to the planet's surface, where the explorers are amazed to find an abundance of food, water and sunshine.
Human Dr. Rush defies orders to interface with the Destiny's computer in a bid to control the ship's flight path, which puts Col. Young in a difficult position. Meanwhile, Lt. Scott, Eli, Chloe and Greer explore a planet's underground ruins.
Lost The Destiny takes off and leaves Lt. Scott, Eli, Chloe and Greer trapped in the ruins of an underground maze, prompting Dr. Rush and Col. Young to devise a recovery plan to save the stranded away team before the ship leaves the galaxy.
Sabotage An expert in hyper drives, who has a past with Dr. Rush, arrives on the Destiny via the communication stones when it seems the ship will run out of power before it reaches its next destination, which would leave the crew adrift.
Pain When the crew suffers from vivid hallucinations that tap into their personal fears, Tamara Johansen isolates the affected from the rest and then tries to seek out the cause of the affliction as it spreads and becomes life-threatening.
Subversion Col. Telford is suspected of espionage after Dr. Rush has a disturbing dream about a covert meeting with the Lucian Alliance. Col. Young investigates the matter with the help of Gen. Jack O'Neill and Dr. Daniel Jackson.
Incursion, Part 1 Young tries to undo the Lucian Alliance brainwashing by interrogating Telford, who reveals the Destiny is in danger of being boarded, so the crew launches a pre-emptive attack. Meanwhile, Kiva tries to force a captive Rush to recreate a dialing program.
Incursion, Part 2 Young and Kiva's confrontation is interrupted as the Destiny is affected by power surges and Rush discovers a binary pulsar emitting radiation that has the potential to kill everyone on board.