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.

Now firmly in control again, Col. Young and the other military personnel try to find a way to live with the civilians who tried to take control of the ship. When the Destiny prematurely comes out of hyper-space due to a computer glitch, they find both a sun and an Earth-like planet that should not be there. Rush concludes that the entire system was created by an alien race that is far beyond their imaginations. With the ship malfunctioning and a month's worth of repairs before it can jump again, several of the military and civilians decide to spend time on the planet. Hard feelings from the mutiny persist and it's an opportunity for everyone to mend fences. When the time comes to return to the Destiny, several of them decide they want to stay on the planet. Young is prepared to let them stay, but he imposes severe conditions.

Dr. Rush relives his past life by sitting in the alien chair in an attempt to download critical data. A university professor, his wife's cancer returns and he is recruited by Dr. Daniel Jackson for what will be called the Icarus project. He's avoiding dealing with his wife's situation and throws himself into his work. In his dream-like state, he's trying to make sense of all the information he is accumulating. Back on the ship, the Destiny comes out of hyperspace and some of the crew investigate the planet below. They find an ancient archaeological site but are trapped when part of the site caves in. Digging them out is a slow process and the next jump is quickly approaching.

Still trapped on the planet after the Destiny has jumped, Lt. Scott, Sgt. Greer, Chloe and Eli try to find a way out of the underground maze. After one is caught in another cave in, the remaining three make their way to a gate but must jump blindly from planet to planet hoping to pick up a signal from the Destiny before it jumps. On board the ship, Col. Young decides to send out a search party. The clock is ticking down and the next jump will take them into an inter-galactic void forever leaving their friends behind. TJ meanwhile decides the time has come to tell Col. Young that she is pregnant with his child.

The Destiny has jumped into hyperspace and is now traveling through an inter-galactic void. They've also been unable to locate Eli, Chloe and Scott who have been left behind. Dr. Rush has calculated that based on their current energy consumption, the Destiny has insufficient fuel to reach the next galaxy and they are doomed to die. The engines suddenly fail however and they arrange for an expert, Amanda Perry, to come on board via the communication stones and help them out. Perry and Rush have known each other for many years but as a quadriplegic, is experiencing what life has to offer. On Earth, Camile Wray's consciousness has been transferred to Perry's body and is wheelchair bound.

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.

Behind the scenes of the sci-fi series, as self-proclaimed superfan Nidai interviews the cast and takes a tour of the show's Vancouver set.

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 is talking into the Kino and showing us around the ship. He enters a room he thinks is the Communications Lab but it is actually the Infirmary. He says that they don't know what half of the machines do.

Eli again is showing us the ship and he enters a room that he has no idea what it is. He says he doesn't think he has been in it before.

Eli shows us his favorite room on the ship, the Stargate Room. He says that Rush believes this Stargate is older then all other Stargates and might be a prototype.

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.

The Kino turns a corner and zooms in on Scott and Chloe having a conversation but they are too far away for the mic to pick it up.

Eli comes up to a hatch marked with 2 X's. He says that if he opened the hatch he would be sucked out into space.

Eli enters the Shuttle and explains that Destiny has two of them but one is inaccessible. He says he is not supposed to be in it because it is for military personnel only.

Eli is interviewing Chloe in her quarters and asking her personal questions. She tells him that nobody cares what her favorite color is because she is not important. Eli disagrees and tries to cheer her up. She says she is tired and asks him to leave.

Eli and Riley are in the corridor preparing for a Kino race. They start down the corridor and turn the corner and Eli's almost hits Camille.

Lt. James enters the shower room and takes off her shirt. She looks up and sees the Kino hovering near the ceiling. She using her shirt to cover the Kino.

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 enters Chloe's quarters and asks if she is okay. She says she really thought they were going home. Scott says that she must be happy to be going to Earth. She says that seeing her mom that way just makes things harder.

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.

Brody is in his quarters and blaming himself for what happened to Riley but Park tells him he couldn't have done anything. Brody says it is all Telford's fault and Rush is right that he is going to get everyone killed. Park asks him what they should do and he says they should help Rush.

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.

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.

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.

Eli Wallace introduces the Destiny's Control interface hub. He calls it "apple core" but this name displeases Adam Brody who demands to call it control interface. Brody tries to get support from Lisa Park and Dale Volker but they also call it "Apple core".

Dr. Lisa Park records a video diary about her time on Destiny and mentions here friends and family. However, she is interrupted and proceeds to have sex with an apparently close male friend.

Eli interviews Airman Kelly, while her consciousness is in Chloe's body, about why she volunteered to use the communication stones.

Dr. Brody attempts to take revenge on Sgt. Riley by playing a prank on him.

Scott tells Greer to be sometimes less formal. After that they chat a bit.

TJ and Dr. Park discuss Rush's relationship with Dr. Perry.

Eli makes another tour through the ship and comes to Chloe Armstrong's room.

Adam Brody secretly share a cigarette with sergeant Spencer.

Eli asks everyone what their "favorite meal of all time" is.

Hunter Riley records his diary entry.

Director Ivon Bartok gives a behind the scenes look at filming the web-only Kino scenes.

Lt. James talks about keeping time on the Destiny. Camile wishes James a happy birthday.

Sgt. Riley uses the Kino to check up on Eli in the infirmary.

Brody, Park, Morrison, Sgt. Riley and Eli recount their most emotionally painful moments in life.

Lt. James documents all the stages she's gone through while aboard the Destiny.