Sam and Sheppard welcome Teyla back to Atlantis after her interview with Mr. Coolidge of the IOA. Coolidge is a new member and seems to be eager to prove his worth, and is distrustful of aliens. He also referred to Teyla as "Honey," which she wasn't thrilled with. Ronon is next, and Sheppard and Sam are concerned. Sam has asked someone to come to Atlantis to coach Ronon: Teal'c. He and Sam make small talk and drop in on an officer and Ronon as they spar. Sam makes introductions but Ronon has nothing to say.
The Wraith arrive on a planet with a Stargate and start working on it.
Teal'c joins Ronon at lunch but Ronon insists he doesn't need a coach to deal with the IOA. Teal'c is skeptical and asks Ronon about how his planet was wiped out. When a furious Ronon pulls a gun on him, Teal'c notes that the IOA will ask similar questions. Sheppard suggests the two of them spar, and a crowd soon shows up to place bets. Sam stops them... until they start up again without the weapons. Sam breaks them up again and calls it a draw.
Teal'c and Ronon depart for Midway Station to meet Coolidge. The Wraith detect the incoming signal as Teal'l and Ronon arrives at the Midway Station where Dr. Lee greets him. The pair will have to wait for 24 hours in quarantine and they're assigned to the same quarters. It doesn't go well.
The Wraith decipher the program coding and launch an assault on Midway. Lee looks on as the Wraith shoot down the guards, then sends out an alert as Teal'c and Ronon watch Three Stooges DVDs. The Wraith sweep through the base but Ronon takes out two of them. The Wraith get to the bridge and take Lee and his assistant/replacement Kavanagh prisoner, and order them to dial Earth.
Rodney and Sam determine that Midway has been cut off but assume it's a malfunction. Rodney determines there was a glitch on a planet near the edge of the Pegasus Galaxy, and figure Teal'c and Ronon are stranded together. Onboard Midway, Teal'c and Ronon start arguing over the best approach, while gunning down Wraith. The Wraith are unable to override the lockout code and Lee tries to explain he can't override it. The Wraith Leader tells his technician to continue work while he prepares to interrogate Lee.
The Atlantis team discover that Midway has an outgoing wormhole, meaning they're unable to dial in. They send a MALP to the planet where the disruption occurred and spot the Wraith equipment before a Wraith soldier destroys the MALP.
The Wraith Leader tries to interrogate Kavanagh, who faints. They prepare to torture Lee for the info, but the technician manages to bypass the lockout code. Meanwhile, Teal'c and Ronon try to get to the control room but spot Wraiths heading for the Gate Room so Ronon goes after them and Teal'c is forced to follow. The Wraith activate the Gate to Earth and prepare to send through a device, using the correct code. A large metal sphere comes through the wormhole, detonates, and knocks out everyone in the base with an electromagnetic pulse.
Rodney determines a way to link back up into the chain of Stargates and Sheppard takes a team to the new planet from which they'll be gating. At Midway, the Wraith prepare to send a wave of soldiers through to Earth. Ronon and Teal'c get to the Gate Room as they leave and go through the Gate after them. The Wraith Leader tries to shut down the gate... just too late. A new wormhole opens to Midway, and Sheppard and his men come through and start searching the base.
Ronon and Teal'c get to earth and find the unconscious SGC staff. Sheppard and his team shoot it out with the Wraith but are unable to get to the Control Room when the Wraith Leader seals it off. The Wraith Leader identifies himself as an associate of the Wraith that worked with Rodney and provided him with the info he needed to intercept the Stargate chain.
Teal'c and Ronon determine that SGC went into lockdown mode and go off to find the Wraith. More Wraith open a wormhole to Midway and Sheppard heads for the Gate Room to shut down the Gate. He gets to the Control Room and finds Lee, but the Wraith Leader has fled. Rodney goes to work while Sheppard goes back out to help his men. Rodney discovers that the Wraith have put a lockout program of their own on the Stargate controls, as more Wraith come through the wormhole.
Ronon and Teal'c discover that the Wraith have been feeding on the personnel, then engage a squad of Wraith and destroy them. On Midway, Kavanagh inadvertently shuts down the system, unaware that it activates the self-destruct. They have ten minutes to stop the self-destruct, while the Wraith try to shut through the door.
Teal'c and Ronon get to the briefing room at SGC where they find Mr. Coolidge, who wakes up. Coolidge insists they call for reinforcements but Ronon and Teal'c refuse, insisting they can deal with the matter.
As the last man standing, Sheppard has Rodney, Lee, and Kavanagh prepare to evacuate the station in a Puddle Jumper, and take out the Wraith by venting all of the air in the station. The major struggles to get to the Puddle Jumper and ends up struggling with a Wraith with his oxygen running out. He guns the Wraith down but collapses.
Ronon and Teal'c shoot their way through the base, taking out the Wraith as they go, with Coolidge following along behind. However, they lose him and split up to cause more damage and locate him.
Rodney tries to establish contact with Sheppard but can't raise him. They repressurize the station. Meanwhile, Ronon finds Coolidge who has contacted the government and has ordered a nuclear attack on the SGC, and insists they head for the escape hatch. Ronon refuses to abandon Teal'c and goes to help him, disobeying Coolidge.
Rodney and the others get to the Puddle Jumper and find Sheppard inside of a pressure suit where he took refuge when the air was vented. On Earth, Ronon fights his way through the corridors and arrives just as the two remaining Wraith attack Teal'c. A vicious hand-to-hand fight breaks out and one of them latches onto Teal'c with his sucker hands... just as Ronon stabs it through the back. They go to tell Coolidge to shut down the nuke, while Ronon and Sheppard launch the Puddle Jumper and evacuate just as the self-destruct activates, destroying Midway.
Later, Ronon meets with Coolidge and the other IOA members and gives them a simple "Yes" when asked if he can obey his superiors. Coolidge acknowledges that's good enough for him. Outside, Teal'c congratulates Ronon on not killing anyone and they prepare to depart on Daedalus to check on Midway. Aboard the Puddle Jumper, Lee and Kavanagh discuss Pearl Harbor, much to Rodney's irritation. The Daedalus brings them aboard and Ronon and Teal'c greet them. Sheppard has sealed himself in the control cabin so he didn't have to listen to the bickering scientists. Ronon wakes him up and brings him up to speed, including the fact that he passed the IOA interrogation.