A week passes by after the events of Justice (in reality for us a few months as the network wanted to wait until after the 2010 Olympics had ended) and Col Young is coming to terms with his decision of leaving Dr. Rush on the barren planet. Camille suspects that Young may have killed Rush due to tensions between the two and she confronts the former about it. When Young decides to report to Earth by using the communication stones, instead of his mind being switched with the body of a Stargate Command personnel, Young finds himself on an alien spaceship!
He watches a blue alien on a platform in the ship. Meanwhile the alien who is now in Young’s body attacks the crew of Destiny. The stone is replaced and the minds are reversed back. What we later find is that Dr. Rush took one of the stones with him and he was found by the blue aliens on the barren planet, when he accidentally triggered a distress signal on the deserted ship on the planet. The aliens have probed Rush’s mind and are now interested in Destiny.
After the ship drops out of FTL drive, they see the aliens mothership following them and soon attacking them by using several smaller ships. One of the smaller shuttles breaches Destiny’s shield and cut a hole on the ship. They abduct Chloe and then take off in their ships. . Scott requests that they send the shuttle back out to retrieve Chloe, as the ship hasn’t tried to depart. Young denies the request. He also believes that the attack may have been a distraction to take prisoners. He wants to rescue her his way, by using the communication stones.
Once again Young uses the stones and switches bodies with an alien on the ship. In the blue alien’s body, Young explores the huge ship and finds to his surprise, a tank in which a very much alive Rush is kept. He frees Rush and convinces the scientist that he is Young. Meanwhile, Young’s body is kept restrained but the stones stop working due to the influence of the alien’s devices. Now the alien on the ship attacks Rush, who overpowers and kills it.
The alien ship begins to attack Destiny again, this time more aggressively. Knowing through Rush that Chloe is also on the ship, Rush goes in search of her and rescues her. Having learned the layout of the vessel, he takes her to the fighter bay. Meanwhile, Greer and Scott, having yet to launch the shuttle, notice that the fighters are retreating again, except for one. Rush and Chloe are in it and climb back aboard the Destiny and reunite with the crew.
In the mess hall, Rush tells Eli, Chloe, Scott, and Volker that after he was able to “free himself” from the “rock slide”, going along with Young’s claim, he entered the crashed ship, and began checking the systems and explains how the aliens found him. Later Rush & Young agree to put aside their differences for the sake of the crew. In the final scene, Rush meets with Wray in the hydroponics room. They both agree that Young is dangerous, and Rush points out that he was nearly killed when he tried to do something about it. She assures him that “Next time will be different.”