Ronon reports to Woolsey, who asks why he hasn't filed any mission reports. Ronon doesn't remember Woolsey telling him to do so. Woolsey gives him a voice recorder to make his reports with. Meanwhile, McKay and Sheppard are running RC cars through the outer base corridors and almost knock over Teyla as she tries to get her son Torren to sleep. She gets him back to her quarters and as McKay and Sheppard head back, the lights go out and they're unable to contact anyone by radio.
Teyla finds herself sealed in her quarters and unable to raise anyone, but the doors open and two men enter and stun her. Meanwhile, McKay and Sheppard meet with other Atlantis team members but are unable to gain entrance to the control room. They discover the stairwell doors are blocked and wonder if someone has infiltrated the base. Zelenka manages to power up the transporters but the one in the control room is locked out. McKay accesses the security cameras, a non-critical system, and discovers there's a Jumper in the control room. They access the camera in the Woolsey's office and find Michael there with Teyla and her baby. He explains how he captured a Jumper and obtained a team's access code. Woolsey let them in and Michael and his hybrids stunned the control room crew then took control of the base.
Michael's hybrids prepare to activate Atlantis' self-destruct systems as punishment but he assures Teyla her son will be safe. As Sheppard orders his men to begin an assault on the control room, Ronon wakes up among the other unconscious Atlantis team members. However, he discovers he's locked up in the room.
One of the hybrids warns Michael that they're having trouble with the self-destruct system and warns it's only a matter of time before Sheppard and the others get through. Michael insists on remaining until they activate it. The soldiers place explosive charges at the doors but McKay warns there's a major energy reading up ahead. The other team moves ahead before they get the warning and Lorne is knocked unconscious. McKay and Zelenka determine Michael has established a stun force field powered from the Jumper and try to figure out how to shut it down.
As Ronon tries to open the doors, Technician Banks wakes up and goes to work trying to override the door lock. Meanwhile, Michael offers to take Teyla along with him and promises not to harm her or her child. Teyla doesn't believe him.
Sheppard prepares to take another Jumper up to destroy Michael's, but McKay has to inform him they haven't repaired the Jumpers they have. Sheppard takes McKay to get one fixed. Meanwhile, Ronon and Banks get out and Banks takes down a Hybrid long enough for Ronon to take it down. As Woolsey and the others wake up, Ronon scouts out the control room and figures out how many they're up against. Woolsey and Ronon take some men to get to the armory only to discover that Michael's men have decoded the self-destruct and are preparing to leave. Ronon tells Woolsey to head back to the others while he tries to stop them.
Teyla grabs a communication device and tries to contact Sheppard while Ronon attacks the hybrids in the control room. Zelenka spots him on the security cameras. Michael and Ronon fight and Teyla runs for it, running into Woolsey. Another Hybrid comes after them and they run, while Michael knocks Ronon off a balcony. Zelenka lets Sheppard know Ronon's condition, and McKay is forced to cobble together parts from both Jumpers to make one functional one with working drones to blow up Michael's Jumper.
Woolsey and Teyla discover the teleporters are locked out. They head down but Woolsey, in the lead, is knocked unconscious by the stun field. A Hybrid comes to investigate and Teyla knocks him down the stairs. She then climbs into an access panel and keeps Torren quiet,
McKay gets the Jumper working but is unable to activate the drones. The Hybrids inform Michael they're unable to find Teyla so he activates the self-destruct with ten minutes until activation. Sheppard has no choice but to crash his Jumper into Michael's. Meanwhile, Michael talks to Teyla over the intercom and tells her he will disarm the self-destruct if she surrenders.
As Sheppard prepare to leave, McKay shakes his hand and wishes him good luck. Zelenka manages to get partial access to the control systems and can drop the Gate shield. They can fly the Jumper up close enough to dial the DHD, create a wormhole, drop the Gate shield, and destroy Michael's Jumper. Sheppard leaves McKay to fly the Jumper while he goes to lead the strike team.
Michael taunts Teyla over the intercom and repeats his offer to take her with him. She finally gives in but tells him to turn off the self-destruct system first. He refuses and informs her he's taken Torren's DNA already. He and his Hybrids go to the Jumper but he pause to kill the unconscious Ronon. Zelenka drops the shield and McKay activates the Gate, destroying the Jumper and the power source supporting the stun fields and the self-destruct. Sheppard and his men attack and gun down Michael's men, while Teyla emerges from hiding. Sheppard wounds Michael, who flees toward the Jumper bay doors. Teyla gives Torren to Banks and goes in pursuit as well.
Michael is trapped in the Jumper bay and climbs up to the roof. Trapped on the ledge, he has nowhere to go and attacks Sheppard. He knocks Sheppard off and he dangles from a support. He pulls himself up and Michael climbs down after him. The two struggle on the lower platform and Michael starts to get the upper hand, until Teyla arrives and knocks him off. Michael dangles from a support beam, and Teyla kicks his hands free. He plummets downward to his death.
Later, Woolsey visits Ronon and commends him for his work. Ronon even filed a report on Michael's attack. Sheppard and McKay are back to RC racing and stumble across Teyla, who says that Torren has slept through the entire assault. Sheppard assures her that with her on the base, Torren has nothing to worry about.