Part 1: When Icarus Base is attacked, its 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 to determine the purpose of the mysterious ninth symbol of the Stargate, which they've never been able to lock in. In going through the Stargate, they are transported not to Earth, but to a very old apparently uninhabited 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. Part 2: Tensions rise as the new arrivals explore the ship. Dr. Rush comes under suspicion with his secretive behavior and attitude. He determines however that the ship is losing air. They find a damaged room that is partly exposed to space but the problem is that the door can only be closed from the inside. Who is prepared to sacrifice their life for the others? Once that problem is solved, Rush determines that the level of carbon dioxide is rising rapidly. The ship comes out of hyperspace near a planet that will have the materials needed to fix the scrubbers. They are given only 12 hours to get what they need.
- A space ship flies through space. Inside there are halls empty and dark. Eventually there is a large room containing a stargate. The gate begins to come alive and eventually a wormhole forms lighting up the room with its light. A military man carrying a gun comes tumbling quickly through the gate. He quickly recovers and scans the room for danger. Then someone else comes tumbling through the gate. He runs over to check on them an is almost hit by a suitcase which comes flying through the gate. More and more people and luggage begin to come through the gate at a breakneck pace, energetically tumbling most of them go sprawling. The man uses his radio "This is Lt Scott, slow down the evac, we are coming in too hot!" A woman grabs Lt Scott and demands to know where they are and why they haven't come through to Earth. Someone calls for a medic, but she's already at work treating someone. A thin man in civilian clothes ascends a staircase and calmly watches the chaos from above. Finally, after the flow of bodies has slowed down a last man comes hurtling through the gate, literally flying through the air. He crashes hard on the deck and Lt Scott and medic, TJ, go to check on him. As the injured man, Colonel Young, passes out he tells Scott "You're in charge".
We flash back to see Eli Wallace, a young slacker, bragging to his friend about how he is going to solve the Dakarran weapons puzzle in an MMORPG called Prometheus. However, when Eli inputs his solution to the puzzle the game simply reboots. Disappointed, Eli is visited the next day by Colonel Jack O'Neill and Dr Nicholas Rush who congratulate him on solving the puzzle and attempt to recruit him. Believing this to a be a joke, Eli refuses and shuts the door in their faces. He is then beamed aboard the space ship General Hammond, which is orbit above Earth preparing to head to the planet Icarus. Rush explains that they had put the Dakaran weapons puzzle in the game as a test to try and recruit people. Rush is the head of a project trying to dial the "ninth chevron" on the Stargate and promises that if Eli joins them that the government will take care of Eli's mother's medical bills. On the trip to Icarus, Eli watches a video which informs him of the history of the Stargate and befriends Chloe Armstrong, an aide to the Senator from California who is traveling to Icarus for oversight reasons.
Returning to the space ship we see the various casualties being treated as well as the desire of everyone but Rush to return home. While unconscious, Young has a memory of his leaving for the assignment, something which puts strain on his marriage. He has a seizure.
In flashback we see the General Hammond arriving at Icarus. Colonel Young calls Lt Scott to escort the arriving dignitaries and Scott breaks off a sexual encounter with a fellow airman to comply. Rush reveals that Eli's solution to the Dakaran weapons puzzle will allow them to finally dial the ninth chevron. However, when the solution is tried it fails to work for an unknown reason.
On the ship, Scott tries to organize the survivors and reveals to them that the life support systems on the ship are failing making the air become more toxic.
On Icarus, Rush puzzles over why the solution failed to dial the gate. During a dinner to welcome Senator Armstrong, the base comes under attack from the Lucian Alliance.
On Destiny, Rush has a showdown with Eli and Marine Masterseargant Ronald Greer over Rush's attempt to turn on the live support system. We see TJ tending to Colonel Young and she has a flashback to Icarus where she revealed her intention to leave the service.
On Icarus, during the attack, things are becoming critical, the attack has made it so the planet is about to explode. However, Rush still wants to try dialing the ninth chevron since this may be their last chance. After a suggestion from Eli he manages to dial the ninth chevron address rather than the planned evacuation to Earth. Rush informs Young of his decision and justifies it by saying that if the planet explodes while the wormhole is connected any blast energy could be transferred to Earth. They attempt to shut down the gate but cannot. Angry, but with no other options, Young orders the evacuation to the ninth Chevron address, telling everyone to take as much of the expedition equipment as they can.
On the ship, they turn on the computer systems. Doing so they discover that the ship is called Destiny and also discover a map showing that it has traversed dozens of galaxies over millions of years and that they are "several billion light years from home".
On Icarus, the people evacuate, carrying expedition equipment with them. Young is the last one through, an explosion sending him flying through the gate.
On Earth, Colonel Carter, who had been directing the space defense of Icarus, learns that the evacuees did not arrive on Earth and wonders where they are.