Amazingly, it looks like the second man isn’t quite dead yet, as he comes to at the sound of voices while Woolsey calls for Dr. Jennifer Keller and a medical unit. He’s still losing a lot of blood, most likely long past any hope of recovery, but Sheppard leans down to tell him he’ll pull through all the same. Laughing bitterly and coughing violently, the airman says he knows he’s going to die, but he’s not going to die without serving some justice. With his final words, he manages to pass on the name he glimpsed on his attacker’s jacket: Hernandez.
Oblivious to their discovery, Capt. Hernandez is eating lunch in the commissary, joking with a group of other newly-arrived personnel when Sheppard steps through the doorway. But his smile quickly fades as Lorne, Ronon, and Teyla draw their weapons and form around the corner table where he’s sitting. Coming up behind the line, Woolsey announces that they have reason to believe Hernandez is involved in an act of sabotage against Atlantis, and they need him to come with them for questioning. He doesn’t want this to turn violent, but with numerous systems compromised and two airmen dead, he’s not about to take any chances. The other men sitting with him slowly stand and slip away, staring back in shock and confusion while Luis stares at Woolsey with disbelief. Leaning close to his superior, Sheppard begins to wonder if maybe they have the wrong guy, but then he’s forced to pull Richard out of the way as a thrown plate flies at his head.
Flipping the table up just as Ronon fires his stunner, Hernandez pushes it forward to smack Lorne in the face and push Teyla off-balance and down a few steps. Then he draws his pistol and begins firing around the side, using his corner position and the thick table to create a makeshift barricade. Bullets ricochet off the walls while other diners stream out of the commissary to escape the shootout. Ronon tries to flank him, but takes a bullet to his right leg in the process, going to one knee on the steps and flinging himself toward an outcropping for cover. Firing a volley of stun blasts into the table edge closest to their quarry, he yells to Sheppard to move in now before this escalates further.
Glancing in the other direction, Hernandez spots Sheppard roll into a flanking position behind another table. He has a clear shot that Luis can’t evade without leaving his own cover and running into Ronon, Teyla, and Lorne. John trains his pistol on the airman’s head and tells him to give up and surrender. The alternative is a bullet in the brain, and he really doesn’t want to send a young man’s corpse to the Dr. Keller. For a moment, it looks like Hernandez might try to fight his way out, but then something appears on his face, in his eyes. He looks absolutely terrified, unsure of himself, staring at the gun in his hand, the chipped walls around him, and at the steel-faced man ready to kill him at a moment’s notice. His hands jitter and his eyes dart around the room before he seems to steady himself and whisper Sheppard’s name and what sounds like the start of an apology. But then it passes, an angry fire leaps back to his eyes, and he shouts that he won’t give them the pleasure of his surrender. Putting the pistol to his head, there’s nothing John can do but watch as he pulls the trigger and tumbles to the ground.
An hour later, Sheppard is sitting in McKay’s lab with his head in his hands, muttering that he should have found a way to stop Hernandez from killing himself. Rodney tells him not to be so hard on himself for the Captain’s death; from what he heard, there was nothing he could have done to save their suspect. At least now they know he was responsible. Sheppard just sighs, insisting that that doesn’t make it any less difficult to absorb. Then he frowns and asks how, if Hernandez was their hacker, there’s still someone in the system throwing up firewalls to stop Rodney from determining where the database was accessed and what was copied. McKay shrugs, suggesting that maybe it’s another virus that was uploaded into one of the high-clearance consoles. Either way, it’ll be shut down all the same once he terminates the correct computer, and he’s almost through the list now. They should have everything finished up in no time, and John leaves to head back to the control room for the scheduled dial-in to Earth.
While the city prepares to report in to the ISGC, most notably a visibly-disturbed Dr. Keller making final notes in the infirmary, Rodney continues plugging away at his work. One by one, he shuts down the last few consoles on his list, but at the third to last one, he suddenly gets success. Surprised at easy it turned out to be, he exclaims that the firewalls dropped with that last terminal’s deactivation, and he can finally access the data he’s been trying to get his hands on. Engrossed in reading over the files, he doesn’t seem to notice that Dr. Kirov’s computer is offline, nor that the young woman is slowly moving closer to his position. He only looks up after realizing that the hack he spent the past few hours fighting wasn’t coded in any programming language used on Earth, but something he recognizes from the Expedition’s second year as Goa’uld (“Critical Mass”). Then he realizes not only that Kirov is continuing to advance toward him, but that it’s her computer he just turned off. He puts it all together a moment too late, asking why it’s always the hot women who go bad before she knocks him out cold. Grabbing McKay’s radio and the pistol Zelenka brought him earlier, she types something on his console and takes one last look around the lab for anything useful before sprinting down the hall.
At the top of the control tower, Woolsey walks up to Chuck and tells him that it’s just about time to start the dialing protocol. Entering from the rear stairs, Sheppard checks his watch and says they should give it a few more minutes for Teyla and Ronon to get there, oblivious to the drama unfolding below. Finally coming to in his lab, McKay glances around groggily before snapping leaping into action. Scanning over the remainder of Kirov’s code, his eyes widen and he tries in vain to counter whatever he’s said. It would appear that she locked his terminal, and he doesn’t have time to waste trying to find the relevant lines of code on the other computers. He goes to grab his radio, then groans when he realizes it’s gone, as is his gun. Checking his watch and hoping he’s not too late, he follows Kirov’s lead and dashes from the lab.
Now it’s down to the wire; Ronon and Teyla arrive in the gate room, and Chuck begins dialing the stargate for Earth. Sticking to the least-crowded corridors, Kirov makes her way up toward them, leaving a transporter and making her way to the control room completely unimpeded. Whatever she has planned, it would appear that it’s about to go off without a hitch. But it’s just than that Rodney barrels into Zelenka near the science labs, nearly knocking him to the floor in an effort to grab his radio. Screaming over the channel, he shouts for them to halt the dialing process immediately, and under no circumstances establish contact with Stargate Command. On the other end, Sheppard starts to ask why, but Rodney’s continued screaming convince him to order Chuck to pause the sequence… just in time, as the eight chevron was about to lock.
Listening to McKay’s explanation as Kirov enters the control room, the rest of the team learn that Rodney discovered a string of Goa’uld code imbedded in the main system. It’s purpose was to upload copied information from the database onto the channel they used to communicate via stargate with Earth. From there it would piggyback onto the ISGC’s computer and transmit elsewhere in the Milky Way. McKay only put it together once he realized that Kirov was the one behind it all along, and then it all made sense. The information stolen from the database was concerned solely with the Ancients’ ninth chevron research and anything even tangentially related to their exploration of the far universe. She had an exotic tattoo she was reluctant to reveal, probably representing her home clan. Her programming, once she lost the luxury of time, was in Goa’uld computer language. And lastly, they know that there’s one group back home with both operatives that could fit both parameters that have the technology necessary to brainwash personnel captured offworld like Capt. Luis Hernandez. If Rodney’s right, “Dr. Lisa Kirov” is actually an agent of the Lucian Alliance.
Turning to where Kirov stands watching all of them at the rear of the control room, Sheppard draws his gun and coldly informs her that she’s going to wish she didn’t make an innocent man take his own life earlier. But just as quickly as his weapon is out, so is hers, and she keeps it trained on the Colonel to dare him to shoot. Everyone watches breathlessly as the two stare one another down, and Kirov slowly moves toward the staircase leading down into the gate room. She says that there’s only one way this won’t end with someone dead, and that’s if they dial the stargate to a planet of her choice in the Milky Way and let her leave. Her gun still aimed at Sheppard as he moves after her, she asks what he’s going to do. Shrugging, John tells her that he’s never going to let her leave this city, no matter how many bullets he needs to take in the process.
Kirov laughs, declaring that if he thought she’d let them take her alive, he’s sorely mistaken. She puts the gun to her head and moves to pull the trigger, but this time there’s no table between the attempted suicide and Ronon Dex. A stunner bolt rings out from the control room and knocks her backwards, sending the pistol clattering down the steps and Kirov to the floor. Glancing up at Ronon appreciatively, Sheppard holsters his weapon and radios McKay to get to work removing that radio piggyback so they can apprise Earth of the situation. It looks like it’s over.
The following day, Sheppard is leaving the detention wing, where Kirov glares back at him angrily from inside a cell. Woolsey and McKay are waiting for him, eager to hear if he was able to glean any information from the interrogation. But unfortunately her resolve was just as strong as it appeared, and she didn’t betray anything besides her undying loyalty to the Lucian Alliance. Filling him in on what they’ve been able to confirm, Woolsey explains that Capt. Hernandez was captured offworld by the Alliance, and the ISGC originally worried he might have been subjected to Goa’uld brainwashing technology. But the fact that the enemy outpost was apparently destroyed in his escape attempt convinced them that it was a genuine escape, and he was already high on the list of potential new transfers to Atlantis. It was an oversight that cost the young man his life, but at least his family can be assured that his killer will see justice.
While they head toward the transporter, Sheppard asks just what the Lucian Alliance was so interested in that it would concoct so elaborate a plot to beam data back to the Milky Way. McKay says that it has a lot to do with the organization’s obsession with the Ancient exploratory vessel currently playing host to nearly a hundred ISGC personnel, the Destiny. They desperately want control of it, and they learned through a mole on Earth that the only concrete information on the ship and how to reach it was found in the Atlantis database. No one’s quite sure how Kirov was able to slip through security to get onto the city before it returned to Pegasus, but given the Alliance’s skill at subterfuge, it’s not hard to imagine. At any rate, the plot was stopped and the stowaway captured. Now they can get back to the business of saving the galaxy, and with a laugh, the three of them turn a corner and head off.