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.
Colonel Young is in his quarters going over paper work. The Kino enters and watches him over his shoulder. He notices it's presence and closes his folder. He tells Eli that even though he gave him permission to keep an eye on things he does not have permission to spy on him. He stands up and grabs the Kino.
Eli shows us his very small sleeping quarters. He says that he hopes it is only temporary because there are more compartments that can't be entered because they are damaged. He says Rush wants them to be fixed but Young wants them to focus on getting home and finding food and water. He says he agrees with Colonel Young and says farewell because he has a calisthenics training session with Greer, who he thinks hates him, in the morning and needs to get some sleep.
The Kino enters the Mess Hall where Scott, Johansen, and Greer are having lunch. Scott says hello and Johansen tells him not to encourage him because he was caught spying on Lt. James. Eli denies it and says that Riley was driving. Greer grabs the Kino and holds it to his face. He warns Eli that if he does it again he will use the Kino to spy on him from the inside.
Becker and Inman are trying to isolate flavorful esters (such as banana flavoring) from chemical impurities in the water from the ice planet in order to make the rations more enjoyable. Becker asks if it is possible to get chocolate but Inman says that it contains over 12,000 chemicals and hasn't been able to be replicated. All of the sudden the ship shakes as if there was an explosion.
Scott and Volker are helping Riley and Brody put on the space suits. Brody thinks he looks stupid but Scott assures him he looks cool. Riley realizes he has to go to the bathroom and Scott tells him to go in the suit because they are designed for it but Riley refuses. Brody gets his helmet on and tries to walk. He takes one step and falls on his face.
While walking down a corridor, Sgt. Ronald Greer and Lt. Matthew Scott (and possibly the entire ship) hear the intercom come on and the voices of Adam Brody and Lisa Park testing something they just invented. The Kino is on Greer and Scott's faces the entire time. It seems that Park rigged a full duplex interface with the Destiny's communication system and the frequencies got swapped somehow and now everyone can hear their conversation. It seems that they should have tested the thing thoroughly before talking bad about the military personnel, who Brody declares "can't walk without dragging their knuckles" let alone work a simple device. Then Brody notices that a light is on, despite Park claiming that the intercom was off.
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.
Eli and Lt. Scott discuss the discovery of the two Kinos found on a Jungle planet - upon the one is a recording of an alternative timeline Matthew Scott. The recording informs the present crew about a disease that was in their water supplies, the native creature on the planet, and its medicinal qualities found in its venom.
Eli Wallace is sitting with Lisa Park, Dale Volker and Adam Brody are watching an episode of South Park from Eli's cell phone, and find one scene hilarious. They are then interrupted by Matthew Scott, who notices that it must have been the fiftieth time they seen the same episode. He came in to announce the start of a morning work out Everett Young proposed to keep the crew in shape. Volker notes he only does his running while being chased, but they still have to run. The team hear that Scott can run two miles in 21 minutes for a man his age, probably faster. Eli decides to wager an energy bar, believing he couldn't do it in time. Scott accepts the bet, and starts the run after Park starts the timer. After Scott leaves, the four continue with the watching South Park, laughing at another scene.
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.
Walking down a corridor aboard Destiny followed closely by a Kino, Ronald Greer hears crying. He pauses and motions for the Kino to turn right. In a room around the corner, Dr. Lisa Park is pacing and muttering to herself about being stupid. Greer indicates for the Kino to remain in the hallway as he approaches Park. He wonders if she is okay, and asks her if Dr. Rush is giving her a hard time. She nods yes, and Greer responds by offering to "bust him up". The two laugh.
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.
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.
Director Ivon Bartok gives a behind the scenes look at filming the web-only Kino scenes.