Becker presents the crew with a root they've scavenged from one of the planets to supplement their rations. Greer pretends to like it to fool the others and then tells them that they need to eat it no matter what it tastes, because it's all they have. He then goes to check up on Spencer, who is late for KP duty. When he gets no response, Greer enters Spencer's quarters and finds him dead. He calls Young, who is meeting with Camille about duty schedules, and tells the colonel that Spencer is dead from a gunshot wound to the head.
Johansen has Spencer's body taken away and does a preliminary examination. She confirms that he's been dead for two hours, was sitting on his bed when he was shot, and his quarters were far enough away from anyone else that no one heard the gunshot. When Camille blames Young for now keeping the unstable Spencer under watch, but Johansen points out that it wasn't suicide: there's no sign of a gun.
Young tells Rush what happened, and the scientists notes that they need to take precautions if there's a killer on the loose. Eli doesn't believe any of them are a murderer, but Rush notes that Spencer had several enemies, no friends, and they're all under stress. He warns Young that they need to find the killer and soon.
In the Gateroom, Young assembles everyone and tells them that they've confirmed that Spencer checked a 9mm pistol out of storage, and that he was shot with a 9mm bullet. The gun has disappeared and the only people with alibis are Scott, Eli, James, Brody, and Park. They were playing cards together and can vouch for each other. Young has no alibi and puts Scott in charge of the murder investigation. Scott calls for a search of everyone's quarters but they protest and insist on being there. The five confirmed innocents split up to search, two rooms at a time. Scott and Eli search Franklin's quarters over the man's objections but find nothing. As they search Camille's quarters, she suggests that they consider Greer the likely suspect. Scott doesn't believe his comrade is innocent, and notes that Greer wouldn't have removed the gun if he was guilty.
Rush calls Young, and the colonel wonders why he didn't come to the Gateroom with the others. The scientist insists that he needs to continue his work and tells Young that he's found new information about the Ancients' chair. Young orders him to get to the Gateroom and then takes a call from Scott. Scott is ready to search the colonel's quarters, but Young insists he doesn't need to be there. Eli and Scott search and Eli finds the gun, hidden behind an air grille. They call young there and show him the gun. Scott doesn't believe the colonel is guilty, but Eli isn't so sure. Young insists that they tell Camille what they found because she'll have to investigate him as the ranking civilian authority, and he doesn't want anything hidden.
Scott and Eli tell Camille what they've found, while Rush looks on. Camille worries that it will look bad for Young, and prepares to contact her superiors via the communication stones. Scott realizes that the Kino should have footage of the ship during the time of the murder and tells Eli to see if it recorded anything significant.
Later, Young hears back from the IOA and calls in Chloe. Camille has been ordered to hold an evidentiary hearing and he wants Chloe to represent him because of her college education. When she wonders why he wants her, Young points out that he wants at least one civilian on his side, and worries that Camille will use the hearing to override him and take command.
At the hearing, Camille has Franklin testify about Young assaulting Spencer when the latter went out of control. Volker testifies that he heard Young discussing Spencer's attitude with Rush, but Chloe questions the accuracy of what he heard. Next, Rush testifies that he doesn't remember what Young said, and implies that Camille might be trying to discredit Young, Young watches the hearing with Eli by remote camera, and realizes what Rush is trying to do. Eli admits that he hasn't found on anything on the footage to clear Young's name or confirm who the real killer is.
Johansen testifies that Spencer was taking sleeping pills, When Chloe attempts to suggest that Spencer killed himself, Camille reminds everyone about the missing gun. She also points out that Young ordered them to conduct an internal investigation rather than let someone use the communication stones and switch places with a forensics expert. Johansen is forced to admit that she has no way to determine if Spencer's death was suicide or murder. Camille calls for a recess and then privately tells Chloe that they need to cooperate and resolve the matter to make sure no one panics.
As Young tours the ship, he overhears the crew discussing the case. They're not convinced of Young's innocence, but some of them believe the killer was justified in removing Spencer.
Chloe lets Scott and his men know that Camille is prepared to call for a vote of the entire crew. When Greer and the others prepare to free Young, Scott tells them to back down. Greer questions his orders, but Young comes in and tells them that he's made a deal. He'll turn over command to Camille in return for her closing the hearing due to lack of evidence.
Rush meets with Camille, who wonders if she's in over her head. He asks for commands of the scientists. She agrees after establishing that Rush will still answer to her. Rush meets with the scientists and they debate the dangers of the chair. Eli warns that it's dangerous but Rush insists that they need it to get back to Earth.
Scott talks to Young, who explains that even if he had been proven innocent, it would have undermined his authority. To keep control, Young would have had to use force. Scott promises to support Young no matter what.
Eli and Franklin discuss the chair and Franklin admits that they can't access the system without the interface. He asks Eli to get him some food so he can get through the end of his shift. Latter, Eli calls Young and tells him they have a problem. Franklin tried to use the chair and is trapped. They manage to free him and Eli explains that Franklin used the chair while he went to get the food. Johansen suggests they use lorazepam and looks to Young for orders. He leaves the decision with Camille, who reluctantly agrees. Outside, Young accuses Rush of pressuring Franklin to use the chair. Rush doesn't deny it but Camille interrupts them and says that it was ultimately her decision. As they go, Eli tells Scott that he hasn't found anything on the footage, but the lieutenant insists that he look harder so they can clear Young's name.
The Destiny arrives at a new planet and engages the Stargate. They confirm the planet will support life and Camille goes to the Gateroom. En route, Greer confronts her and observes that she's had him and his men taken off the away team roster. Camille denies suspecting him of Spencer's murder and tells him to get out of her way. He does but warns that the matter isn't over. She then puts Volker in charge of the four-man expedition and assigns Dr. Caine, Vanessa, and Rennie to the team.
Eli calls Scott to let him know he's found a discrepancy in the footage time codes. Some of the footage is missing, and Scott calls Young in to take a look.
On the planet, Volker and the others find the wreck of an alien ship. On the ship, Rush hears of the discovery and is eager to investigate. As he goes to the Gateroom, Young stops him and takes him to the room where Eli, Scott, and Camille have gathered to watch the deleted footage that Eli has recovered from the backup. It shows Spencer using a Kino to record his final words and then shoot himself. Scott and Eli figure that someone with the necessary technical expertise, one of a dozen potential suspects, then took the gun and wiped the Kino footage. Camille apologizes to Young, but Rush would rather investigate the ship. Young agrees and takes command, and leaves with Rush for the planet.
On the planet, Volker reports that they've confirmed the alien ship doesn't belong to the Ancients. The hatch is sealed and they don't have enough time to get through it before the Destiny leaves. Rush asks for a few minutes to work with it. Young agrees and sends the others back, and Rush explains that if they can get inside the ship, they may be able to gain valuable information and technology. Young prefers to discuss how Rush erased the footage and took the gun. Rush admits that he did it to set up Young to make him appear guilty, so that Camille would take over. The scientist insists that Young isn't capable of making the important decisions to get them back to Earth. Young attacks Rush and knocks him done, and then asks if they're done. A bleeding Rush says that they'll never be done, and Young knocks him out and leaves.
As the Destiny goes back into hyperspace, Young just makes it back through the Stargate. He tells Camille that Rush was caught in a rockslide and killed. Camille returns command of the crew to Young, given the evidence. As the others leave, Young tells Eli to store the Kino footage on a flash drive and erase all other copies. Eli reluctantly agrees.
Rush wakes up and discovers that it's now night time, and he's been abandoned. He looks up at the sky in shock and horror, realizing that he's alone.