- "We've been informed that this ship faces an incursion from armed forces of the Lucian Alliance, the group responsible for the attack on Icarus Base. All military personnel aboard have been placed on high alert. If the enemy has acquired the means to dial Destiny, their point of ingress will be the Stargate. So the gate room is off-limits. All surrounding corridors have been placed on lockdown. No one may enter without proper authorization. I've provided Homeworld Security [Command] with intelligence on the planet from which the Lucian Alliance intends to launch their assault. They're dispatching forces as I speak."
- —Everett Young
As a result of switching with Colonel David Telford using the Long-range communication device, Dr. Nicholas Rush gained fragments of memory from Telford's mind indicating that he was a spy for the Lucian Alliance. Since Telford worked undercover in the Lucian Alliance for a year prior to his work at Icarus Base, it is assumed that the Alliance converted him using Goa'uld brainwashing technology. After consulting with Colonel Everett Young, Rush decided to try and make contact with the Lucian Alliance members on Earth to expose and capture them. To do this, he switched with Telford during the next scheduled use of the device.
Young, not completely convinced that Rush was being honest, arranged for Rush to be followed covertly by Dr. Daniel Jackson, and in the meantime kept Telford occupied. Rush managed to make contact with the Lucian Alliance, but his lack of knowledge in their protocols revealed his duplicity and he was captured. Before Daniel could arrest the Alliance members, they escaped in a Tel'tak.
Rush was tortured for his identity by Commander Kiva. Rush eventually broke and told her his name. Knowing who he is from Telford's reports, Kiva forces him to work on the Alliance's own research into dialing the ninth chevron, which had thus far been stalled due to their lack of the power regulation equation found by Eli Wallace.
Revealed as a traitor, Telford was interrogated on the whereabouts of Rush by Young, but Telford denied any wrongdoing. Young brought in Lt. General Jack O'Neill in the body of Cpl. Marsden to speak with him, since O'Neill had seen the effects of Goa'uld brainwashing before. Confronted by O'Neill, Telford admitted his role as a spy proudly. Seeing this, O'Neill authorized Young to use more drastic measures to break Telford. Young had the air vented from Telford's room, bringing him to the edge of death, then revived him, thus breaking the brainwashing. Telford warned Young of the impeding Lucian Alliance invasion and gave him the coordinates of the planet where their ninth chevron research was set up.
The George Hammond was dispatched to the Lucian Alliance outpost to stop the invasion. Unable to beam the occupants out due to jamming devices, Colonel Samantha Carter dispatched a squadron of F-302 fighter-interceptors for a ground assault. By this time Rush had made enough progress to dial Destiny at the cost of destroying the planet. Her hand forced by the attack, Kiva ordered the ninth chevron to be dialed and sent her men through, taking Rush with them. Carter was forced to leave two of her 302s behind to escape the destruction of the planet. The F-302 pilots and over 100 of Kiva's men were killed in the ensuing explosion, but the rest get through the Stargate to Destiny safely. (SGU: "Subversion", "Incursion, Part 1")
Traveling to Destiny severed the communication link, returning Colonel David Telford and Dr. Nicholas Rush to their original bodies. Commander Kiva attempted to kill Telford, still believing him to be Rush, in retribution for the deaths of her people, but Telford convinced her that he wasn't Rush by using the code-word he used to identify himself that Rush didn't know. Telford also pretends to still be brainwashed. Having been informed of the attack, Young was prepared. The Gate room was locked down and the atmosphere ready to be vented with the push of a button. However, the presence of Telford's body made him hesitate, and he instead decided to give them a chance to surrender. Young used the intercom to request their surrender, but his hesitation buys them the time they need to escape using specialized lockpicks to open the doors.
A firefight ensues between the two groups. The Alliance forces their way into the surrounding corridors, capturing ten Destiny crewmembers, among them Lt. Tamara Johansen, Sgt. Hunter Riley, and Cpl. Rivers. Four Alliance members are captured by the Destiny crew. Eli Wallace and Chloe Armstrong are forced to escape through an elevator, ending up near the bow of the ship where there's air but no active life support. Chloe also has a gunshot wound on her leg and is losing blood.
The two sides are at a stalemate. Kiva has hostages but Young still controls life support. In an attempt to trick Kiva, Telford leads a small group through one of the damaged sections to flank the Destiny crew, covertly informing them of his plan so they'll be lying in ambush and will be able get the drop on the Alliance. Before this plan can be realized, however, an intense burst of gamma rays vaporizes one of the Alliance soldiers, followed by a ship-wide power disruption. The plan is called off until the cause can be found. When Kiva learns of the soldier's death, she asks for medical supplies as a show of good faith to prove the Destiny crew didn't do it. Young attempts to use this opportunity to end the invasion, but the plan is foiled by another power failure. Kiva kills Rivers in retaliation.
It is discovered that Destiny has stopped within range of a binary pulsar which is emitting deadly bursts of radiation every 46 minutes. It is these bursts which are causing the ship to temporarily lose power, since Destiny is rerouting power to reinforce the shields. The Faster-Than-Light engine is also offline, preventing them from escaping. A plan is devised to reroute shield power from the side of the ship opposite the pulsar, but it needs to be done from outside the ship. Lt. Matthew Scott and MSgt. Ronald Greer are chosen to do the work.
The fastest way to the shield emitter on the hull is through a breach in Kiva's section. She leverages this for control of the ship. Telford convinces Young to go along with her request until he can transfer control back to Rush and Dr. Adam Brody, who take refuge in another control room. However, his plan goes awry when he is caught in the act by Kiva and they both shoot each other. Telford's bullet hits Kiva's liver, mortally wounding her, while Kiva's bullet passes clean through Telford, non-fatally injuring him.
Assuming Young's people to be responsible, Dannic rounds up the military to execute them, leaving Scott and Greer trapped outside. Rush reroutes them to another section of the ship near Eli Wallace's location, so Eli can let them in through an airlock. In the makeshift infirmary, Airman Armando Elsinor Von Spelker the Third attempts to overpower an Alliance soldier. The soldier's gun goes off in the struggle, hitting T.J. in the stomach.
Before Dannic can carry out the execution, Varro intercedes, as they need the crew alive. With TJ wounded, they need the crew to use the Long-range communication device and call in trained doctors. Camile Wray, Dr. Dale Volker, Ryder, and Kemp are forced to switch with Dr. Brightman, Dr. Timan, Dr. Zeigler, and Dr. Finch to treat the wounded. Telford is saved, but Kiva dies from her injuries. TJ also recovers, but her baby is lost. Varro convinces Dannic to send the expedition members through the Stargate to a habitable planet, except for the people still connected with the doctors. He also argues that they should keep TJ, as she would die if moved and could be valuable later. Varro and several loyal to him are later sent through the Gate to join the expedition members, as Dannic believes they are working against him.
Scott and Greer manage to survive the radiation burst by hiding on the underside of the ship, and once back inside go on a recon mission. They observe the expedition members being sent through the Stargate via a Kino. Chloe's gunshot wound mysteriously heals while Eli is gone, and she and Eli are sent to join Rush and Brody. Rush has concocted a plan to get rid of the Alliance. By transferring power away from the shields, they can force the Alliance to negotiate. Though the radiation is deadly to them, too, the Hydroponics lab is deep enough inside the ship that they could survive by barricading themselves inside. With most of the crew off the ship, only the Alliance will be in danger. Scott and Greer plan a rescue mission for the few left on the ship.
Scott and Greer's rescue mission is cut short when they are pinned down by Alliance soldiers. Rush has the door to the Hydroponics lab sealed, and orders Dannic to surrender, fully willing to sacrifice the lives of his fellow crew members if it means retaking the ship. Dannic refuses to listen to reason and intends to call Rush's bluff. Ginn realizes how insane Dannic is, and kills him then surrenders on the Alliance's behalf. (SGU: "Incursion, Part 1", "Incursion, Part 2", "Intervention")
After the surrender, the crew is retrieved. The Alliance soldiers are imprisoned while Colonel Everett Young decides what to do with them. With the shield restored, Destiny is able to jump to FTL and reach its next destination. Young decides to leave them on the next habitable planet, but at the insistence of Homeworld Command and the International Oversight Advisory, keeps a select few as potentially valuable sources of information, including Varro, Ginn and Simeon. Those that remain, after a period of continued imprisonment, were slowly integrated into the crew (particularly Ginn) in exchange for revealing information about Alliance activities in the Milky Way, though its revealed that Simeon is only pretending to cooperate. Later, Simeon, who is revealed to have held the information about an attack on Earth the whole time, escaped, killed Ginn and killed a few members of the crew before finally being killed by Dr. Nicholas Rush. When the attack on Earth does come, Varro is instrumental in disarming the Naquadria bomb the Alliance get to Earth via Tel'tak. (SGU: "Intervention", "Aftermath", "Pathogen", "Trial and Error", "Malice", "Alliances")