On the bridge, Young tells the scientists that he's willing to give Rush a second chance and understand his point of view. They confirm the structure in the background radiation that Rush has identified, possibly constructed by intelligent beings. They bring Rush in, and Young explains that he's consulting with the scientists. They've dropped themselves out of FTL near three planets. Young suggests that Rush gets some rest and apologetically insists that he'll let him know when they have something. As everyone prepares to explore, Eli asks Young how much longer Homeworld Command will be questioning Ginn, and then hastily withdraws the question out of embarrassment.
Rush goes to see Dr. Amanda Perry, who is using Ginn's body via the communication stones. When he gets no response, he goes into her quarters and finds Ginn, dead.
James uses a communication stone to make contact with Earth. Meanwhile, Johansen, Young, and Eli come to Ginn's quarters, but there's nothing they can do. Scott confirms that Simeon has escaped lockdown and killed his escort, and is now loose on the ship. Simeon shoots out the power conduits and takes out two guards at the armory, and starts collecting Lucian weaponry in storage.
Johansen tells Rush that they don't know for sure what may have happened to Amanda on Earth. Young starts organizing search teams, and James calls to tell them that she's confirmed that on Earth, Amanda's body is dead. She also tells them that before she died, Ginn told Homeworld Command important information.
Rush leaves and angrily punches the walls as he makes his way through the ship. Eli asks Young for a gun, but the colonel tells him to wait there.
Simeon shoots more soldiers and gets to the Gateroom, and takes Park and Volker prisoner. He orders Volker to seal the doors, cutting off Rush before he can enter, and then has the scientist dial the Stargate. Simeon then forces Volker to tie up Park and takes her through the Stargate. Brody gets the Gateroom door open too late for Rush to stop the Alliance soldier, so Rush grabs a kino remote and goes through after Simeon.
Scott and his team get to the Gateroom and Volker tells him what happened.
Rush arrives on the barren planet and finds Park kneeling in front of the Stargate. She warns him that there's something on his back, and Rush confirms that it's an Alliance bomb with a proximity fuse. There's no sign of Simeon.
Johansen and his team get the injured men to the medical ward and try to stabilize them. One of the men dies before Johansen can get to him.
As Scott prepares to go after Rush and Simeon, Young arrives and tells him that they need Simeon alive. Ginn told the Earth authorities that Simeon knew the Alliance' plan of attack against Earth. Before the squad can go through, Rush calls to tell them that they need to wait until he defuses the bomb. While he works, Simeon draws a bead on him and waits. Young sends a kino through to watch the situation as Rush defuses the bomb. He realizes that he can't do it without a pinpoint tool, but uses the wire frame of his glasses to improvise. He gets the bomb off and throws it away where it harmlessly explodes.
Young sends his men through, while Rush walks off and the kino follows him. Scott goes after him into the nearby hills. Simeon fires at both of them, disabling the kino.
Young goes to see Varro and tells him what happened. Varro insists he had no idea what Simeon had planned, and that Ginn and Simeon were from the same clan. Only they knew about their faction's plans for Earth. Varro warns that Simeon is supremely dangerous, and they might be better off letting Simeon go rather than risk more deaths.
Rush searches for Simeon and stumbles across another proximity bomb. He gets away just in time, and Scott follows the explosion. He tells Rush that they need Simeon, but Rush warns that Simeon won't tell them anything. As Greer arrives, Scott calls James and has her form two search parties to explore. Scott then asks Rush if he's going to help, and warns that they need Simeon alive. Once they capture Simeon and get the information they need, Scott tells Rush he can do whatever he wants. They have nine hours until Destiny jumps back into FTL, and Scott gives half that time to search before the return back to the Stargate.
On the bridge, Brody and Volker discuss what happened. Volker feels guilty, and Brody suggests that Simeon left him alive to suffer emotionally. Eli comes in and tells them Young wants them to stall the clock. Park arrives and insists that she's fine, and assures Volker that he did everything he could.
Johansen finishes in the medical tells Young that she could only save three of the men. He puts a hand on her shoulder, comforting her.
As they search, Scott asks about the signature. Rush explains that it might be a message from God, or something far more inexplicable. As Rush goes, Greer insists that he'll never forgive Rush. Scott figures that Rush may be right, and they need the knowledge to return home, but Greer warns that Rush better watch his own back.
Brody informs Young that they can't stop the clock, but Destiny will stop after four hours and they'll still be in range. On the planet, Rush tells Scott and Greer the same thing. They spot a herd of indigenous animals.
Chloe is still in quarantine, working on Rush's equations. She looks up at Destiny jumps to FTL.
As the three men continue their search, Rush finally breaks down and cries helplessly. Scott sends Greer on ahead and then tries to comfort Rush, saying that the scientist couldn't have known what would happen, and that he couldn't trust Rush with his secret. The lieutenant admits that they're going to have to work together and put aside their differences. Scott then suggests that Simeon will probably die on the planet, but Rush warns that he has a kino remote and can use it to jump back to the Lucian Alliance via the Stargates. Simeon opens fire, pinning the three men down. James is close and tells Scott that they're moving in on Simeon.
Chloe calls Eli on the radio and tries to console him, but he insists he doesn't have time. He snaps at Volker and tells Chloe that he'll talk to her later. Brody says that they have to drop out, and Eli snaps at him and tells him to do it. They have eight hours on the clock. Park tries to comfort Eli, who tells her to leave him alone.
As they take cover, Rush manipulates his kino remote. James and her two men approach the ridge where Simeon opened fire. Much to Scott's surprise, Rush stands up and exposes himself. Nothing happens, and he tells Scott to order them back. James and her men start to run as another bomb goes off. They survive, but two of them en are injured. Scott orders James to take them back to the Stargate. Rush claims that he guessed Simeon had left, but Scott accuses him of lying. The scientist admits that he just realized how to use his kino remote to track the one that Simeon has.
Young discovers that Eli is preparing to go to the mission and hunt down Simeon. Eli warns that he has no chance of stopping the clock, and even if he did, the consequences could be incalculable. Young insists they can save lives on Earth, but Eli doesn't believe that Simeon will tell them what they want. When Eli asks for a gun, Young tells him that he's not a killer, and that killing would change him. He asks Eli to go back to the bridge, and Eli relents.
Scott and the others spot Simeon in the distance. Greer shoots him in the leg, but Rush tells him to kill him. As Simeon gets over the ridge, Scott tells Rush that Greer did the right thing to save lives back on Earth. However, Rush insists that Simeon will never tell them what they need to know. Simeon returns fire, wounding Greer. Rush continues going after Simeon, ignoring Scott's plea on the radio that it's too late and they need him.
Young brings Chloe to the bridge, and she explains that she's slowly been gaining control of the pathogen within her. She was able to translate Rush's algorithms, and insists she can help. Brody warns that she could slip a virus into the programming, and Young tells them to watch everything that Chloe does.
Simeon cuts the bullet out of his leg and then calls Rush on the radio. He boasts that Rush will have to live with the lost of his loved one, just as Rush's people killed Simeon's friends. Simeon says that he left Rush alive so he'd suffer, but if Rush comes after him then he'll put him out of his misery once and for all. Rush keeps coming.
On the bridge, Chloe blanks out and starts programming the computer with new information. Eli and Brody stop her, and she snaps out of her trance. Chloe insists that it's okay, but Eli points out that she has no idea what she just did, and no control over what's happening with her. As he sends her back to her quarters, Brody checks the programming and says Eli has to look at it.
Rush catches up to Simeon as he crosses a barren field near more of the herd animals. The scientist then takes out some of the C-4.
Scott gets Greer back to the Stargate with two hours remaining.
Rush tries to shoot Simeon with his handgun, but misses repeatedly. Simeon returns fire, forcing Rush to take cover. As Simeon limps toward him, Rush sets off an explosive charge, panicking the herd animals. They stampede, trampling Simeon. Rush walks out and confronts the wounded man, who says that he has information. Rush shoots him once in the head and walks away.
Over nine hours later, Rush returns to the Stargate. He's surprised to discover that Scott and the other soldiers are still there. Scott explains that Eli figured out how to track the kino remote signals, and verified that both remotes were coming toward the Stargate. Rush claims that he believed Eli would stall the clock. However, Scott says that Chloe calculated a new course and turned the ship around to get Rush. The lieutenant realizes that Rush gave Chloe the calculations, and hopes that Rush was right about how Simeon wouldn't talk. Otherwise, they've endangered millions of lives. As they go, Scott asks Rush if he feels any better, but Rush doesn't respond.