A SGC research team on an alien planet comes under attack and is forced to evacuate through a Stargate set to a distance universe via the ninth chevron. They find themselves aboard an Ancient vessel billions of light years away, a vessel with waning life support and no signs of life.
The Icarus Base survivors assess their supplies and try to determine their chances of survival. The odds decrease sharply when they discover that air leaks and contaminated carbon dioxide scrubbers mean that they have less than an hour of air left. With time running out, one of them will have to make the ultimate sacrifice to buy the others a chance to live.
Scott and Rush take an expedition to a nearby planet to find the lime necessary to repair the carbon dioxide scrubbers aboard the Destiny. With time running out before the ship goes back into hyperspace, the team splits up. Meanwhile, Chloe uses the communication stones to speak with her mother about the death of Senator Armstrong, and Telford attempts to assert his authority among the survivors while occupying Young's body.
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. Meanwhile, tensions sweep through the ship as Rush has a breakdown, some of the crew demand answers from Eli, and Telford returns to judge Young's competence to command.
As the Destiny plummets toward the sun, Young calls for a lottery to determine which seventeen survivors will take the only remaining shuttle and escape to safety.
When the Destiny's water supply mysteriously dwindles, Scott and Young are forced to explore an ice planet to replace the missing liquid. While they're gone, a mysterious swarm of creatures are discover and attack a crewman.
When Young, Eli, and Chloe use the communication stones to return to Earth, Telford is put in command of the Destiny with orders to try a risk procedure to power the Stargate and return everyone to Earth.
The crew of Destiny explore a planet and find a kino showing them being attacked by alien creatures and wiped out by a disease. However, despite the fact they avoid traveling to the planet, they discover that the same disease is now wiping out the crew.
While Greer discovers a piece of Ancient technology that may hold the secret to getting them home, Scott and Camille use the communication stones to settle their personal lives on Earth.
When a crew member is killed, what appears to be a suicide soon turns out to be possible murder. When Young is implicated, Camille takes command on behalf of the IOA and holds an evidentiary hearing.
A new race is revealed when Young's consciousness is accidentally transported to one of their ships.
Camille and her people make their move to usurp control of the Destiny from the military.
Destiny unexpectedly drops out of FTL when it encounters an uncharted star. When they discover a planet capable of supporting life, the crew must decide whether to stay or continue.
When Rush tries to access the Ancients' chair of knowledge, he finds himself in a dream state where he must relive his wife's slow death from cancer to learn the ship's master code. Meanwhile, Scott, Eli, Chloe, and Greer explore the ruins of a new planet and find themselves trapped.
Scott, Eli, Chloe, and Greer are left behind when Destiny departs without them on its preprogrammed course. While Rush struggles to find a way to rescue them, the team escapes the maze only to realize that they must somehow find a way to catch up to the ship before it departs the galaxy. Meanwhile, Johansen has personal news for Colonel Young.
One of the ship's 16 FTL drives overloads, exploding and dropping the ship out of FTL. While a brilliant scientist switches places with Camille to come aboard and make repairs, the crew begins to realize that the overload may not have been an accident.
Johansen tries to track down what is causing the members of an away team to hallucinate. Things take a turn for the worse when the hallucinations spread to other crew members.
Rush's dream reveals the identity of a traitor. While Rush uses the communication stones to go to Earth and follow the clues to locate the traitor's superior, Young interrogates the traitor on Destiny and demands answers... no matter what the price.
The Lucian Alliance manages to open a Stargate to Destiny and are forced to evacuate to the ship. While Young must cope with the incursion, Eli and Chloe are stranded in a distant part of the ship, and ship systems begin to collapse.
With time running out as the ship's systems malfunction, Young's people must work with Kiva and her men to save the ship before they all die.
Scott and Greer are seemingly killed while on the hull of Destiny; Rush tries to undermine the ship's shields to force the Lucian forcess to surrender; Chloe makes an amazing recovery; T.J. finds herself on an alien planet with her baby; and the Lucian forces disagree on how to maintain their hold on the ship.
Rush secretly gains access to the ship's hidden bridge and brings Destiny out of hyperspace so they can get food at a nearby planet. However, Rush miscalculates and the shuttle crashes. Meanwhile, Young and Camille disagree over how to deal with the Lucian prisoners.
The crew encounters another seed ship, and Destiny auto-docks with it. They realize that it may hold the key to them getting home... but it also holds a deadly danger.
While Eli and Camille travel to Earth to deal with personal issues, the Destiny crew realizes that Chloe has become possessed by an alien intelligence... and it wants to learn everything about the ship.
Scott is infected by a highly contagious plant organism, and can't be brought back to Destiny for fear of infection. As the crew on the planet try to improvise a cure, more of the plant organisms close in... and Scott hallucinates that he's in the town of Cloverdale on the day before his wedding.
Young is plagued by mysterious dreams where Destiny is destroyed by alien attackers no matter what he does.
Destiny encounters an alien derelict, and Rush and Young board. But when they're stranded, Young confronts Rush about what he's hiding.
Simeon kills Dr. Amanda Perry when she is using Ginn's body, and he escapes from Destiny via the Stargate to a nearby planet. Rush goes after him, intending to kill the man who murdered his lover. Meanwhile, a distraught Eli tries to stop the countdown clock so that Destiny can remain within range.
The others who chose to remain on the alien construct planet appear in the shuttle, floating in space next to Destiny. Young must decide what to do with them, and determine if they are who they claim. Meanwhile, Chloe tries to make her peace with Scott and the others as the alien pathogen continues to transform her.
The crew uses their control of Destiny to investigate radiation signals, and discover a graveyard of ships, leftover from some great battle...and not all of the ships are dead. Meanwhile, an old friend returns at the ship's time of greatest need, and Chloe continues to fall under the sway of the alien pathogen.
Destiny survives the battle against the drones thanks to Chloe summoning the aliens that have been pursuing them, but the crew realizes that they are out of options... and turning Chloe over to her former captors is their only choice.
In the wake of the Cluster attack, the crew must consider abandoning Destiny, and Eli comes up with a way to dial the ninth chevron. However, as they begin evacuation proceedings, a Rush from 12 hours in the future arrives to warn them that they're pursuing a fatal plan of action.
Camille and Sgt. Greer switch bodies with a visiting senator and scientist, but are trapped when Homeworld Command comes under attack by the Lucian Alliance. Meanwhile, the senator assesses the viability of Destiny.
While waiting to regain contact with Earth via the communication stones, Chloe's body is taken over by a foreign consciousness. While the crew tries to deal with the repercussions of this new presence, Johansen finds herself faced with a medical dilemma.
Richard Woolsey of Homeworld Command tries to convince the government of the planet Langara to dial Destiny and establish a supply line, but Telford and Young suspect that they have already made an alliance with the Lucian Alliance. Meanwhile, Rush and Amanda try to find a way to be together physically.
A team from Destiny is attacked while exploring an alien planet, and two crew members are abducted by a native creature. While Greer is forced to team up with Varro to recover them, on Destiny Eli and Brody examine newly-discovered stasis pods and get in over their heads.
To evade a wave of attacking drones, Destiny enters FTL and comes upon a planet settled by the descendants of the Destiny crew from the alternate timeline.
The Destiny crew take the Teneran settlers, the descendants of their counterparts from the alternate timeline, back to their homeworld of Novus, only to discover that the civilization has abandoned the planet due to extreme volcanic activity.
When the command ships blockade stars along Destiny's path, the crew must find a different, superhot star to recharge at. Eli and Rush are forced to pilot the ship in, while the rest of the crew evacuates to a nearby planet... only to discover that the drones are already there.
The crew of Destiny must make a final and potentially fatal decision to evade the command ships and continue along their designated course to find ultimate answers.