Rush wakes up in bed next to his wife, Gloria. He gets up and writes down some notes while she sleeps. When she comes out to the kitchen later, she finds him hard at work on his calculations. Gloria reminds him of their appointment with Dr. Browning at 4 and he writes it down. However, then he tells her that he can't make it today and goes to his study, which is covered with calculations.
At the college, Rush addresses a lecture hall of students... and glowing lights start to fill his vision, distracting him. Afterward, one of his co-workers, Constance, approaches and asks why he didn't go to the oncologist with Gloria. Rush lies and claims that Gloria wanted to go on her own. In his office, Rush sees the lights again but they disappear after a moment. He then gets a call from Gloria, who tells him that the cancer is back. As he listens to her, Rush works on his formula and sees the lights again. She asks if he's coming home and he vaguely tells her that he'll be there soon.
When Rush arrives home, he finds Gloria playing the violin. He turns around leaves without talking to her. He goes back to the college and Dr. Daniel Jackson comes over to talk to him. Rush has been trying to avoid him because he doesn't want to help him unlock the ninth chevron. Daniel is surprised that Rush knows so much since the project is classified. Rush explains that it's already happened and he's just reliving everything as a dream due to a side effect of a process he can't control. As Daniel stares at him in silence, Rush walks away.
Young comes in to check on Rush, who is sitting in the Ancients' knowledge chair. Johnansen confirms that the scientist's life signs are stable, and Brody explains that Rush didn't want to involve anyone else. He explains that they modified the chair to avoid damaging the subject, and they can't wake up Rush externally. Only Rush can safely do it, and Brody notes that Rush would have done it whether he helped himself or not. Young prefers to focus on the modification and whether it can damage the ship, and Brody admits he doesn't know. He then explains that they created a buffer to slow down the data flow and make it safe, and then let Rush access it later as a dream. There's an implanted trigger, a door, that Rush has to pass through in the dream to wake up. Young tells them that if anything goes wrong, he's pulling the plug.
Rush returns home and finds Constance telling Gloria to take a plane home. She says that she doesn't have the strength. Rush ignores the conversation and goes to his study to continue his work. Constance comes in and he tells her that he's busy, and he doesn't want any distractions. She can't understand why Rush doesn't care, and he insists that he can't explain.
Chloe goes over to see Eli and ask if they're okay. He claims there isn't a problem but she notes that he's sitting by himself. She promises that she won't betray him again and he seems to accept that. The ship drops out of FTL and they go to the Gate Room. The kino shows ruins on the nearby planet, but no signs of life. They have six hours until Destiny leaves. Eli and Chloe both volunteer to go, and Eli explains that Chloe has been studying archaeological findings and wants to go. Young informs them it's okay and chuckles as they leave.
Rush addresses his class about the code that he's trying to work, and encourages them to help. They have nothing to say and he starts ranting, insisting that they're all him and they should be able to help. When they have no idea what he's talking about, Rush orders them all out. Daniel appears in the room and says that it's not their fault, and Rush admits it's his fault that he can't solve it. Daniel asks him again if he wants to work with the ninth chevron, and Rush tells him that he left his wife to die while he ends up in deep space. Worse, he's angry that Eli managed to solve it despite his lack of ambition. Rush thinks Eli should be there now trying to solve the code. Daniel talks about how he lost his wife, and Rush admits that the data comes faster when he's with her. However, Daniel tells him he should take the time to be with her. Rush goes back to work, and his nose starts bleeding.
Scott, Greer, Chloe, and Eli go to the planet and start exploring the ruins. On the ship, Johansen treats Rush's nose bleed and admits to Young that she doesn't know exactly what it means. The colonel considers pulling Rush out prematurely, and Brody isn't willing to calculate his colleagues odds of survival.
At home, Rush tries to work and Gloria talks about her appetite. She finally asks why he's there and Rush explains it's because it's what happened before. Gloria tells him not to let her illness hold him back. As he gets up and takes her hand, Gloria assures him that she knows he'll be there for her when the time comes.
Eli sends the kino down into the tunnels beneath the ruins. Scott and Greer are less than interested, but Eli suggests there might be something there they need to survive. Chloe starts lecturing them on archaeology and Eli admits they don't have kino footage because he lost it in the maze of tunnels. Scot reluctantly agrees and Greer offers to stay behind, but Eli jokingly asks if he's scared. Greer goes down with them, covering from they rear. As they descend, Scott explains to Chloe that Greer is a little claustrophobic.
As Rush and Gloria take a walk in the park, she asks for a chance to sit down. He continues to work on the code as she undergoes treatment, while accompanying her on treatments and going to church. At home, Gloria continues to give violin lessons as long as she can but can only cry as she sees Rush constantly ignoring her.
Scott's team descends further but he finally orders them back. As they go back, Greer spots an oversized alien spider and opens fire. The shots bring down the ceiling, cutting them off from the exit.
Aboard Destiny, Young makes contact with the team via radio. Scott briefs him and Young sends a team to get them out. However, they have less than two hours before the ship jumps to FTL. As Scott blames himself for agreeing to enter the tunnels, Eli and Chloe explore briefly but find no exit and can't locate the kino. James arrives with the rescue team and she tells Scott that it doesn't look good.
Rush wakes up from a dream of Gloria and finds Daniel there. Daniel points out that his nose is bleeding again, and then informs him that they have the location of a planet suitable for the Icarus Project. Rush asks him if he understands any of his code work and Daniel admits that he doesn't. The scientist explains that all of the code is data stored in the ship's memory banks. He now believes that staying won't make it any clearer. As he goes to the door to leave, Daniel asks him how Gloria is doing. Rush admits that Gloria is dying today, and Daniel asks why he isn't with her. When Rush wonders why he keeps asking that, he realizes that the day is April 6. The telephone rings with the doctor informing him that Gloria is dying, but he hangs up and goes back to his work. Gloria didn't die on April 6, and Rush realizes that the address of his house has changed to 46. Daniel suggests that 46 is twice 23, and represents the theory of the 23 Enigma. As Rush thinks back, he realizes that he's seen 46s everywhere. He wonders if it has actual significance, and then collapses, clutching at his chest.
With less than 30 minutes remaining, Young calls to inform James that she's running out of time. Eli begins to panic and wonders what they're going to do.
On the ship, Johansen determines that Rush had a cardiac event and warns Young that he can't take much more. Young believes that if Rush has learned the master code, he might be able to delay Destiny's departure. The best chance for the trapped crewmen is to pull Rush out prematurely.
With time running out, James calls Scott and says they're going to use C-4 to blast apart the debris. He and the others as far back as they can and she sets off the charge. The tunnels collapse in a wide area, making things worse. She apologizes and he tells her to get her team back to the ship before it's too late. She reluctantly agrees.
Rush goes to the hospital where Constance is sitting with the dying Gloria. Constance leaves them alone and Gloria realizes that he's not there for her. She points out that he chose the memory because it's one he doesn't want to remember, and figures that he's just there for his answer. When it becomes clear Rush would rather die than fail, Gloria wonders how he's changed. Rush admits he's always been able to make the hard decisions, and insists he has good reasons. She points out that her death made him callous, and he's not the man she loved. Gloria tells him to listen to his own conscience, and not let her death change him. When she mentions how she's dying because a gene passed on by her mother failed to repair damaged DNA, the door appears. Rush takes her hand and Gloria assures him that she knows how much he loved her, and asks him not to take it out on others. He promises her that he'll never stop loving her.
In the chair, Rush wakes up and Young tells him what's happening. Rush admits that he can't do anything about it and Young calls Scott and the others to tell them. The colonel tells them not to give up. He and the others can only watch as the wormhole shuts down as the ship goes into FTL, leaving the four crew members behind. On the planet, the team waits for their inevitable deaths.
Young goes to see Rush, who is back at work. He explains that he may have found a clue to give them control of the ship. The number 46 represents the number of chromosomes in human DNA. The Ancient sensors scan for specific genetic markers, but they had no way to crack the code... until now. The Ancients used their own genetic code, and they can run through the variations. It will still take time, but it's a chance. As Young goes, he asks Rush if it was worth risking his life. The scientist merely says that they'll see.