As part of the plan to extend ship's rations, Becker is preparing a potato-like root that they've found on a planet, Greer hesitantly tries it and then proclaims it safe and raves about the taste. The others quickly discover he's lying about the taste and Greer tells them to get used to it, because it will at least keep them alive. Greer discovers that Spencer is late for KP duty and calls him on the radio, but gets no response. He goes to Spencer's quarters and finds the sergeant lying on the bed.
Camille is reviewing the duty schedules with Young and warning that they may be too intense. Greer calls Young and informs him that Spencer is dead from a single gunshot wound to the head.
As the body is carried away, Johansen does a preliminary examination and places the time of death within two hours. She believes that Spencer was sitting on his bed when he shot himself, and his quarters were far enough away that no one heard the shot. Camille insists that Young should have kept Spencer under watch, but Greer points out that it wasn't suicide because there is no gun.
Later, Young and the others inform Rush of Spencer's death. He points out that if it's murder, someone must be responsible and they should take appropriate precautions. Eli finds it hard to believe any of them could be a murderer, but Rush points out that they're all under stress and Spencer didn't have any friends among the crew. He warns Young that they'd better find the killer, and quickly.
Young assembles everyone in the Gateroom and tells them what they've discovered. Spencer was shot with a 9mm gun that he checked out of storage, and it has since disappeared. He goes over the alibis of the crew and confirms that Scott, Eli, James, Brody, and Park were together playing cards. Since Young has no alibi, he puts Scott in charge of the investigation. Scott orders a search of everyone's quarters for the weapons, but the majority of crew insists on being there when their individual quarters are searched. The alibi'd group splits up to search two rooms at a time. Scott and Eli start with Franklin's room, and the scientist isn't thrilled at the implication. However, they find nothing in his quarters.
Eli and Scott search Camille's quarters, and she insists that Greer is the obvious suspect. Scott notes that they wouldn't have any evidence of murder if it wasn't for Greer, and believes he's innocent.
Rush calls Young and tells him he has new information about the Ancients' interface chair. Young notes that Rush is supposed to be in the Gateroom with the others, but Rush explains he'd rather be working. Young tells him to get to the Gateroom and then gets a call from Scott saying it's his turn. Young chooses to remain in the Gateroom. Scott gives the room a casual once-over but Eli spots the gun, hidden in an air vent.
They call Young to his quarters and tell him what they've found. Scott insists that Young wouldn't have hidden the weapon and believes his superior is innocent. Eli isn't convinced, and Young tells Scott to show Camille the gun. Since Scott can't investigate a superior officer, Camille is the civilian commander. Young tells Scott to turn over everything so they don't get caught in a lie.
Scott and Eli take the gun to Camille and brief her. Rush and Camille worry about how it will look. Scott realizes that Eli put the kino on automatic search and tells him to review the footage for any evidence. Camille goes to use the communication stones and contact her superiors for advice.
Later, Young calls Chloe in to his quarters. he explains that the IOA told Camille to hold an evidentiary hearing. Young believes that Camille will use the hearing to get herself put in command, replacing the military authorities. The colonel asks Chloe to represent him, both because of her training in political science and because he wants to have at least one civilian on his side as he clears his name.
The hearing begins and Camille calls upon Franklin to testify that Young once assaulted Spencer when the sergeant went out of control. Next, they call Volker who overheard Young and Rush talking about Spencer's disruptive attitude. Chloe points out that Volker may not have heard the conversation correctly and they call Rush to the stand. He claims not to remember the exact words that Young says, and notes that Camille wants him to imply that Young viewed Spencer as a disruptive influence that needed to be removed. Scott and Eli watch the televised hearing and Scott notes that Rush managed to imply it without saying it himself. Eli hasn't found anything on the kino footage to prove Young's innocent, or identify the guilty party.
Next, Johansen testifies that Spencer was taking sleeping pills. Chloe tries to establish that Spencer may have killed himself but Camille points out that the gun was missing. She also notes that they could have brought in a forensic expert via the communication stones, but it was Young who ordered the investigation among themselves. Camille presses Johansen and gets her to admit that whether they had an expert or not, the lack of forensic equipment would make it impossible to determine if Spencer's death was murder or suicide. Camille asks for a recess and confronts Chloe, insisting they need to resolve the matter to reassure everyone.
As Young walks down the hallway, he hears several crewmembers discussing the case. None of them are sure if he killed Spencer or not, and some support Spencer’s removal.
Chloe goes to see Scott and the other marines and informs them that Camille wants everyone onboard to consider the evidence and vote. Greer is prepared to end the situation once and for all, insisting that Young is being set up for a lynching. Scott orders him and the others to back down. Greer refuses but before they can resolve the matter, Young arrives and tells him that he's made a deal with Camille. She's going to close the hearing due to lack of evidence. In exchange he's turning over command of the crew to her.
Rush goes to see Camille and congratulate her. She wonders if she's in over her head and wonders what he wants. Rush asks for and receives command of the scientists, including Eli, and Camille agrees once she confirms he'll still report to her. He then meets with the scientists and they examine the Ancients' chair. They debate the dangers and Eli warns that it's usually proven near-fatal. Rush insists that mastering the chair is the solution to their problems.
Scott goes to see Young and ask what he's trying to do. Young admits that Camille might not have enough to convict him, but she could have undermined his command. He refuses to try and rule the ship by force. Scott insists they need a real leader, and tells Young that the military will support him no matter who is in command.
Later, Eli checks on Franklin, who is examining the chair. Franklin admits they've had no luck altering or slowing down the data feed. The system is designed to resist any access other than through the chair. He asks Eli to get him some food until Rush arrives to relieve him.
Young is reading in his quarters when Eli calls and informs him that they have a medical emergency. The colonel and Johansen go to the chair room and discover that Franklin is in the chair. Rush and Eli are trying to free him. The chair finally releases him and Eli explains that he was gone for five minutes, and when he returned, Franklin was in the chair. Young looks at Rush, who has nothing to say.
Johansen tries to treat the comatose Franklin and suggests she could try a high dose of lorazepam. She looks to Young, who lets Camille make the call. Camille tells Johansen to do it. Outside, Young confronts Rush and accuses him of pressuring Franklin to try the chair but reminding them it was the only solution to their problems. Camille interrupts him and says it's ultimately her responsibility, and Young insists that he knows that all too well. As they leave, Scott asks Eli to find something on the kino footage, but Eli tells him there's nothing there. The lieutenant insists that Young was framed and they need to clear his name.
emerges from FTL near a planet and opens a wormhole. Brody sends through a kino and confirms the planet will sustain life. He contacts Camille, who leaves her quarters to go to the Gateroom... and finds Greer outside. He notes that she's taken him and several other marines off the away team duty roster, and accuses her of believing he killed Spencer. Camille says it's his problem if he thinks that and tells him to get out of her way. He does, but whispers that he's not going anywhere.
In the Gateroom, Camille puts Volker in charge of the four-man expedition, puts Dr. Caine on the team, and assigns Vanessa and Rennie as marine security.
Eli calls Scott in and tells him that he's discovered a discrepancy in the time codes. Someone has deleted footage from the time that Spencer was murdered. However, Eli backs up the footage every two days for his documentary. Eli accesses the footage and upon seeing it, Scott calls Young to take a look.
On the planet, Caine is about ready to give up. However, Volker and the others find something ahead: the wreck of an alien ship.
Back on the ship, Rush gets word about the discovery. With two hours before the Destiny
goes back into FTL, he heads for the Gateroom. Young stops him and says they have something important to discuss. He takes Rush to where Eli, Scott, and Camille have recovered the footage. It confirms that Spencer recorded his final words and then shot himself. Scott points out someone took the kino and the gun, and Eli admits there's a dozen people on the ship who could have deleted the footage, Camille apologizes to Young while Rush insists the situation can wait until after they explore the alien ship. Young agrees with him and overrides Camille, and then insists he's going with Rush to the planet.
The two men head across the desert to the ship. Volker has determined it's not an Ancient vessel, and that they don't have enough time to cut through the hatch. Rush asks for a few minutes and Young agrees, and sends the others back. Once they're gone, Rush explains that the ship's creators could provide them with the information and technology they need. Young, unimpressed, tells Rush that he knows the scientist took the kino and the gun and erased the footage. Rush admits that he did, and that he knew there wouldn't be enough evidence to convict Young. He points out that Young is the wrong man for the job, unwilling to make life and death decisions. In response, Young attacks him. Rush fights back, hitting Young in the head with a rock, and the two men struggle. Young easily beats him down and asks if they're done. Rush insists they'll never be done, and Young knocks him unconscious and walks away.
With seconds to spare, Young returns through the Stargate and tells the others that Rush didn't make it. As Johansen treats his head wound, Young tells Camille that they were caught in a rockslide and Young barely managed to escape. Camille informs him that given the new evidence, she believes he should take back his position as commander. As the others leave, Young asks Eli to stay. He tells him to put the rest of the kino footage on a flash drive and erase everything. Eli agrees and walks away.
Night on the planet, and Rush wakes up. He realizes that he's been abandoned and looks up at the night sky in horror.