When Icarus Base is attacked, it's inhabitants are forced to flee through the Stargate. The base was created on a distant planet to take advantage of a powerful energy supply located there. Their goal is to try and determine the purpose of the mysterious ninth symbol of the Stargate which they have never been able to lock in. In going through the Stargate, they are transported not to Earth but onto an very old, apparently uninhabited but huge spacecraft. With the group's commander injured, Lt. Scott and the chief scientist, Dr. Nicholas Rush lead the exploration of the craft. Several areas of the ship have been damaged but it is basically functional. They are able to learn that they are in fact billions of light years from Earth.

With the air supply failing on the Destiny, a team disembarks to a desert-like planet in search of the mineral needed to scrub the ship’s air of carbon dioxide. After testing numerous sand samples without success, and with their window of opportunity closing fast, the group opts to split into two to cover more ground, despite the unbearable heat.

The Destiny suffers a power crisis, putting the lives of the stranded crew in jeopardy and forcing them to consider abandoning the ship.

With the situation onboard the Destiny dire, General O'Neill and Home World Command orders Col. Young to execute a high risk plan concocted by the I.O.A. scientists which, in theory, could return the crew to earth.

Aboard Destiny, Dr. Rush supervises the exploration of new areas of the ship. Looking for resources to make their everyday lives easier, the crew stumbles upon a piece of Ancient technology that carries the promise of a way home. While somewhat familiar with the find, Dr. Rush can’t guarantee the safety of using it, bringing him and Col. Young to a standoff on what to do.

Earth's Stargate Program isn't the only group in the Milky Way that's interested in the Ancients' Destiny. What's worse, this long-time foe may have a spy among those closest to the Icarus project.

An enemy from the Milky Way has boarded the Destiny and has taken hostages. Is it possible that they know how to get back or have they stranded themselves as well?

As Young and Camille attempt to resolve the hostage crisis with Kiva, Destiny suffers from power fluctuations and blackouts due to its proximity to a binary pulsar.

Everett and the crew continue their efforts to save Destiny while holding off the Lucian Alliance invaders.

Desperate for food and water, Rush directs the ship to a planet that has been locked out of Destiny's controls. Young and Wray clash over what to do with the Alliance prisoners.

The crew encounters a ship remarkably similar to Destiny, which may hold the key to their returning home.

When Scott's team explores a new planet, a plant-like organism infects the lieutenant, causing him to hallucinate a life back on Earth where he is getting married.

The crew's new-found control over Destiny's flight path introduces new risks when they find themselves in the middle of a war between two races.

Locked in a battle with a Drone Command Ship, the Destiny is surprised by the arrival of the Aliens that abducted Rush and Chloe.

Rush travels back in time to avert a disaster, meeting a past version of himself.

Camille and Sgt. Greer are trapped when Homeworld Command comes under attack.

Chloe's body is taken over by another consciousness. Meanwhile, Dr. Volker is stricken with a mysterious illness.

Rush slips into a coma in the neural interface chair, and Amanda connects with him in the ship’s matrix, but Ginn informs Eli of a problem with that scenario. Elsewhere, Dr. Rodney McKay’s plan to dial the ninth chevron address hits a snag.

The Destiny needs to be refueled but every time they come out of FTL the drones seem to be waiting for them. It's not obvious how the drones know they're there but it doesn't matter a great deal since they only have one more try before running out of fuel completely. Eli suggests they go through a blue supergiant star, though the heat it creates might destroy the ship. They have little choice so Col. Young evacuates everyone to the only planet available with the exception of Eli and Rush. Lisa also stays behind to collect some of the medicinal herbs they've grown only to be trapped just as the Destiny goes through the star. On the planet, Young and the others find evidence of a destroyed civilization - and the drones.

Eli and Rush have found a way to identify the location of drone mother ships using the Destiny's long range sensors. The bad news is that the Drones seems to be awaiting them at every possible stop along Destiny's path. They find a temporary solution to neutralize the mother ships but realize that they cannot engage in a major battle every time they need to re-supply. Eli suggest that they use the stasis pods for the crew and jump to the next galaxy, a trip that will take three years. All goes well until they realize that one of the pods has been damaged and one person will have to stay behind in the hopes of fixing the unit in the short time available or die.