In a rare glimpse of life before the Icarus Project, we see Nicholas Rush during his wife's final battle with cancer. Gradually, we realize that the scene is merely a memory that Rush is reliving - in reality, Rush has strapped himself into the chair that will download Destiny's information into his brain.
Aided by Brody, Rush has modified the ship's interface to moderate the speed of information downloaded into Rush's brain, in hopes of keeping him alive. When Colonel Young finds out, he is furious he wasn't informed, and threatens to pull the plug if anything goes wrong with the ship - even though that could end Rush's life.
In Rush's subconscious journey, his dying wife is desperate for his attention, but he, in turn, is solely bent on solving the equation of Destiny's systems. The man who recruited Rush for the Stargate program appears - but Rush is able to change the course of their actual conversation. He lashes out, saying that he has no time for the program, as his wife is dying. The government man, in return, surprises Rush by telling him that he should spend more time with his wife.
Destiny drops out of FTL to find a planet covered with ruins, but no signs of life. Chloe and Eli accompany Scott and Greer on their exploratory mission. Eli suggests they explore the planet's underground tunnels for resources. Greer and Scott are opposed, but Chloe and Eli convince them it'll be worthwhile. Greer, plagued by claustrophobia, is edgy, and when a predatory alien spider appears, Greer opens fire, causing the ceiling to collapse and trapping the quartet in the system of tunnels. Young sends a rescue team - they rig C4 to create a new egress, but this only makes things worse. With less than half an hour left before Destiny jumps back to FTL, the rescue team has no choice but to return to the ship.
Rush, suffering from nosebleeds and heart palpitations, is about to give up on finding the key to Destiny's code when the Stargate recruiter urges him, again, to be with his wife. Rush then uncovers a mysterious anomaly: The number 46 keeps coming up. In the control room where Rush's body is being monitored, Young urges TJ and Brody to keep him in the chair in hopes that he can find the code and stall Destiny's jump back into FTL - otherwise, Scott and his team will be lost.
Rush reluctantly visits the altered memory of his wife on her dying day. She is now a part of his subconscious, and makes him evaluate his morality since her death. He begs forgiveness, and she tells him to move on, saying her death was just an accident of genetics, but this leads Rush to an epiphany. The number 46 is the number of genes in the human genetic code, and with this clue, Rush leaves the download. Immediately upon Rush's awakening, Young asks him to stop the ship from jumping, but Rush is unable to do so. Young delivers this news to Scott, and his team take in their fate as the ship speeds away.
Rush is back at work as soon as possible, and shares the information with Young that the number 46 in his download means that Destiny's code is based on Ancient genetic code. With this information, they'll be able to control the ship. Running through the permutations could take days or years, but there's hope, even though they had to leave Scott and his crew behind.