When the command ships and their drones cut off all access to planets, the Destiny crew must find a way to escape their enemy once and for all.
As Greer looks on, Johansen checks on Park's eyes to see how she is recovering from the flash blindness she suffered when Destiny entered the blue giant. However, Park still can't see. Young, who has watched the exchange, leaves and Camilla warns that he's running the fine edge of exhaustion. Young ignores her advice and meets Rush and Eli in the interface chamber. They explain that they've found a way to track the drones. Camilla figures that they can now find a safe star to refuel at. However, Eli demonstrates that the command ships and drones have blockaded every Stargate between their current location and the edge of the galaxy.
Young and Rush use the communication stones to go to Earth and tell Telford what their situation is, and that they have no way to go off their path and find a viable planet. They only have a month of supplies and ask Telford to set up a supply line via the Stargate. However, Telford warns that they've had no luck getting the Langarans to risk themselves to power the ninth chevron.
Chloe discusses Park's situation with Johansen, who warns that Park's retina were damaged by UV rays. Chloe says that it's not Johansen's fault, but Johansen says that sometimes you have to play the hand you're dealt. Chloe insists that there is hope for both Park and Johansen, but Johansen vividly describes the symptoms of ALS, leaving her trapped inside of a paralyzed body. She concludes by saying they all have to play the hand they're dealt.
Rush and Eli tell the scientists what they've discovered, and Rush proposes that they focus all of their efforts on one command ship and prevent it from notifying the others. He has an idea on how to keep them from taking damage, and they meet with Young, suggesting they dial up the shields. If they can match the proper shield frequency to the drone's incoming fire and override the ship's random shifts, they can reduce the amount of damage. They know the frequency because of the drone that they brought onboard. Young notes that if they're wrong, they'll effectively have no shields at all, but Rush insists that they're not wrong.
Destiny prepares to come out of FTL and attack a command ship, and Rush overrides the shields and sets them to the proper frequency. Chloe programs the FTL dropout and they come out on a collision course to the command ship. They barely avoid hitting their enemy, and the command ship launches drones. Their firepower is ineffective and the crew open fire on the command ship. They manage to damage but not destroy it, and Destiny is rocked by explosions. They realize that the drones are flying right into the ship on kamikaze runs. The command ship tries to outmaneuver them, but Destiny comes around and manages to destroy it. The drones go dormant and Young sends away teams to the shuttles to check the planet for supplies. Eli warns Rush that they can't do that every time they resupply, and Rush admits that they need to come up with a new plan. They get what supplies they can and leave before more command ships arrive.
As Young goes to his quarters to get some sleep, Eli approaches him and says that he's come up with a plan. He suggests that they skip their current galaxy with one continuous FTL jump around the galaxy to reach the next one. However, he admits that in their current condition, it will take three years. Young notes that they only have a month's worth of supplies, and Eli responds by suggesting that they enter the stasis pods that he, Brody, and Rush found weeks earlier. Rush explains that the jump will require every ounce of power they have, and if Eli's calculations are even a bit off, they'll drift for thousands of years. However, if they don't do it soon they won't have enough power to even make the attempt. Young tells them to make the preparations, and gives Rush 24 hours to come up with a better idea.
Young breaks the news to Camille, and she recommends that everyone have one last visit to Earth via the communication stones to say their goodbyes. The colonel agrees but says that they have to do it quickly.
As Rush tries to work out calculations for an alternative, Chloe visits and tells him that Eli's calculations are solid. He objects, saying that if they go off the path set by the Ancients, they could miss all the knowledge in-between that they were meant to accumulate one piece at a time. Chloe agrees, but points out that if they don't go through with the plan, the ship will be destroyed and it will all be for nothing.
The first group prepares to enter stasis with Johansen monitoring their progress. As he enters his pod, he tells Johansen that he'll see her soon. Brody activates the stasis procedure and the first group is successfully frozen.
Eli goes home to visit his mother and tells her that he has just enough time to say goodbye. He explains what they're doing and that they'll be out of contact for three years. Eli blames himself for his choices, worrying that he's abandoned her, but his mother assures him that he's living his life and that now she understands. She assures him that he doesn't need to be there as long as she knows that he's happy, and Eli admits that he is despite everything.
Brody calls Volker and has him run a diagnostic from the bridge.
Young returns to his quarters and tries to get some rest, but is interrupted when Volker comes to tell him that last section of stasis pods have taken damage and they can't be brought online. They don't have enough pods for everyone and are eight short. The scientists meet and tell Young that they need palladium hydride, found in meteorites, and the one planet they've found is locked out because the meteorites have made it inhabitable. Worse, a command ship is in the system. They can override the lockout, but they can't defeat the command ship without eliminating any chance they have of making it to the next galaxy. Even worse, they don't have enough power to support eight people out of the stasis pods.
Park and Greer discuss the situation, and she tells Greer not to suicide himself. She gets an idea and asks Greer to take her to Young. She tells Young that they can drop off an unmanned shuttle nearby, mimicking the signal of a Stargate dial out, and the command ship will attack. While it does, they can dial in and get the palladium hydride. Eli suggests they rig it to self-destruct, taking out the command ship, and Young agrees to the plan.
Once they arrive in the system, the crew launches the shuttle and then head for the planet. Greer and Scott prepare to leave with Morrison, but the scientist warns that they won't be able to test for suitable concentrations. All they can do is get one kino sled worth of the palladium hydride. Once the command ship goes after the shuttle, Scott takes his team through and Rush prepares to time the explosion of the shuttle to the last second necessary. They put the shuttle on evasive maneuvers, while the away team starts collecting samples.
Rush orders Eli to take the shuttle toward the command shuttle and Rush sets off the explosion, blasting both ships apart. Scott and his people return with the ore and Brody confirms that they have what they need.
Camille comes to get Scott concerning his goodbye trip to Earth, and Scott admits that he barely knows his son Matt, and that he doesn't believe that the mother Alicia is a good parent. He's received assurances that Homeworld Command will step in if Scott doesn't feel she's doing a good job. Scott asks Camille what she plans to say to Sharon, and she admits she was only able to talk to her on the phone. She said that she was sorry and that it wasn't fair to her anymore, and that Sharon should just move on. Sharon had no response other than to cry.
The next group enters the stasis pods.
On Earth, Chloe shares a hug with her mother.
Park sees a lake using her borrowed body's eyes.
Scott watches Mark and Alicia leave their house but can't bring himself to approach them.
The next group of crew say goodbye to each other as they enter the pods.
The remaining eight crewmembers eat the remaining food and offer a toast. Young says that they're a family now, whether they like it not. He tells them that they are the smartest, most compassionate people that he's served with and they all share a toast.
Before entering the pods, Scott and Chloe share a kiss. Greer assures Young that he's fine. Camille tells the colonel that he'll finally get some sleep. Young has Johansen enter her stasis pod, and then Rush and Eli activate the pods. The colon el then reports back to Telford one last time, and says that he won't be visiting Emily. He admits that his marriage was broken a long time ago and he had no one to blame but himself. Telford assures Young that they'll still be there for them in three years.
When Young returns, Eli and Rush explain that they have discovered that one of the pods is damaged and they're one short. They try to bring the pod back online without success, and Rush talks privately to Young. Later, Young then tells Eli that Rush has calculated that if two of them enter the pods now, the remaining person can survive for two weeks. Rush wants to do it, but Young says that he can't trust him so he'll have to be the one to stay out. Young says that he's the only choice, but Eli says that he has at least a small chance of fixing the pod. He finally admits that he's smarter than Rush, and won't take no for an answer.
Later, Eli listens to music in his quarters when Rush comes to see him and says Young told him what they discussed. Eli wonders if Rush volunteered knowing they wouldn't accept, and Rush admits he didn't anticipate Eli taking his place. He believes that they'll need Eli on the other side, and tells Eli that he has tremendous potential. Eli insists that he isn't throwing it away, and says that there's no point in having potential if he doesn't step up to use it. Rush admits that Eli has come a long way and leaves.
Rush says goodbye to Eli and Young and enters his pod. Once they freeze him, Young asks Eli if he's sure, and Eli says that he's never been more sure of anything in his life. They embrace and Eli places the colonel into stasis.
Systems shut down across the ship. Eli looks out the observation port and smiles as Destiny goes on its way.