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.

The survivors arrive on an uninhabited ship floating billions of light years away from Earth. Panic spreads throughout the group and Col. Young, who was severely injured during the escape, transfers command to Lt. Matthew Scott, before lapsing into unconsciousness. Teams led by Dr. Rush and Sgt. Greer try to make sense of the situation, while Lt. Tamara Johansen, a medic who was days away from leaving the program, is thrust into the role of chief medical officer.

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 ship on a collision course, the crew must decide who will stay and who will flee on the shuttle to try and find a habitable planet.

Severe rationing can't save the Destiny's dwindling water supply, forcing Colonel Young and Lieutenant Scott to seek out drinkable water on a deadly ice planet.

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.

Visiting a newly discovered jungle planet, the crew is amazed to recover a Kino by the gate. Downloading the Kino data, Eli discovers video of the team, which appears to have been shot during an earlier visit. The mystery of the video’s origin becomes a secondary concern as members of the team start falling ill.

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.

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.

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.

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.

Dr. Rush struggles to determine why Destiny has no record of this star system while Col. Young directs Lt. Scott and a small team to shuttle down to the planet's surface on a fact finding mission. Upon landing, everyone is amazed to discover that the atmosphere and terrain are idyllic. Relishing the sunshine, fresh air, clean water and abundance of food, many are reluctant to return to the ship, believing that providence has intervened.

Risking his life with a piece of Ancient technology, Dr. Rush finds clues to unlocking more of Destiny during flashbacks to his life back on Earth before Icarus, with a wife dying of cancer and meeting Dr. Daniel Jackson to learn about the Stargate. Meanwhile, members of the Destiny crew find themselves trapped while exploring tunnels on a nearby planet.

Trapped on a planet in rubble and left for dead, Ronald Greer must do everything he can to save himself. His ordeal brings back tragic memories of his past with his abusive father and loving mother.

When one of the twelve FTL drive modules on the Destiny explodes due to an overload, the crew calls upon a brilliant scientist from Earth to help find a solution.

Dr. Tamara Johansen tries to track down what is causing the crew to hallucinate.

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.