The timely arrival of the Daedalus, lead by Col. Steven Caldwell, saves Maj. Sheppard's life from a suicide bombing run, but it may not be enough to defeat the Wraith when more hive ships are on the way. Thankfully with the new ZPM, McKay might pull off another miracle.
Strange malfunctions begin to occur when members of the expedition return from a trip to Earth aboard the Daedalus. When things go too far, they discover that the ship has been infected by a Wraith virus, and now it has the instinct to stay alive, even if it means it has to kill.
Following a lead on the whereabouts of Lt. Ford, Lt. Col. Sheppard and Teyla get captured by Ronon Dex, a man who they find out is a runner, hunted by the Wraith. When they offer to help, the team must face off against their old ally, and possibly gain a new one.(This is the 200th Stargate episode).
After the team witnesses the aftermath of a culling, a Wraith Dart suddenly appears. When it's shot down to preserve Atlantis' secret, they discover that McKay and a female marine officer were beamed aboard, whilst their drastic measures to save them has left the consciousness of the female marine officer trapped in Dr. McKay.
Sheppard's team stumbles upon a technologically advanced society that purposely leaves their criminals on a penal colony near the Stargate, for the Wraith to discover them first. But after the prisoners shoot the jumper down, they discover that the situation is more complicated than it first appears.
After having found an experimental Ancient power generator, McKay becomes obsessed to triumph where the Ancients failed, but the price might be too high. Elsewhere, Teyla and Ronon go to the planet Balkan to trade, but discover that not all of Ronon's people died.
While investigating a planet, the team comes across a Wraith girl who has been raised by her human "father," hiding from the people of the nearby village in fear of her life. But she doesn't consider the consequences when she takes an incomplete drug to turn herself human.
After Ellia injects him with the retro-virus (Instinct), the Atlantis team races against time to find a way to reverse Sheppard's transformation into an Iratus bug hybrid. But even though Sheppard might make it difficult for them, he could be the key to his own salvation.
The team finds an Ancient warship still inhabited by Ancients in suspended animation. They are all connected together through a virtual environment, that Sheppard enters to communicate with them. The only problem being, the Ancients think that their virtual lives are reality.
Sheppard's team is kidnapped off-world, only to find that their captor is none other than Ford. He has recruited several men into taking the Wraith enzyme, and now they intend to use the team to destroy a Hive Ship to prove the "glorious" effects of the drug.
After the attempt to destroy the Hive backfires, the team becomes captured by the Wraith, demanding answers. Meanwhile, Dr. McKay takes a massive dose of enzyme and escapes to Atlantis in a state of frenzy, but his choice could put him on the edge of death.
Sheppard gets pulled into an Ancient device, separating him from the rest of his team and the outside world. While trying to get him out, the team discovers that time moves much more quickly inside and Sheppard could die of old age before they release him.
It is discovered that The Trust have infiltrated Atlantis and planted a bomb inside, set to go off the next time they dial Earth. To add to the tension, two Wraith cruisers are on the way, and Dr. Weir wants to figure out if there could be a Goa'uld spy in Atlantis' midst.
During the test run of a recently repaired puddle jumper, it crashes deep into the ocean, leaving Dr. McKay sinking underwater. When he shows the first signs of losing hope (and sanity), he must rely on a hallucination of Lt. Col. Samantha Carter for his survival.
The team finds a world that possesses Ancient technology, but only the royal family may be allowed to operate it and lowly villagers are treated with little dignity. When he tries to set things right, Sheppard finds himself a pawn in the rivalry between the heirs to the throne.
After recovering two alien stasis pods from space, the minds of the inhabitants are transferred into Dr. Weir and Sheppard. But when it's discovered that the two are enemies hoping to settle an ancient score, the alien combatants put the entire population of Atlantis in danger.
Ladon Radim comes to the expedition wanting to overthrow the Genii leader, Cowen. They are reluctant to help, but it seems he has discovered a ZPM that he could trade with the expedition. Later, Radim's true motives are revealed... for the time being.
An amnesiac young Lieutenant in Atlantis, Michael Kenmore, suffers poor treatment from the personnel, and disturbing nightmares that he is a Wraith. Yet things become worse, when he accidentally stumbles upon a shocking discovery about himself... he is one.
The team comes to aid a civilization taking refuge throughout an Ancient outpost. While trying to repair systems, McKay discovers a volcano below the outpost that will obliterate life on the entire planet, suggesting evacuation. Yet during the process, the Stargate is destroyed.
A Wraith faction (including Michael) contacts Atlantis to seek help in destroying their common enemies, the Wraith. Because the Wraith are currently engaged in a destructive civil war, they suggest using Atlantis' retro-virus to turn their native foes into human prey.
Production
"Runner" is the last episode where Rainbow Sun Francks is credited as a regular cast member. Jason Momoa joins the main cast in this episode.
While rehearsing scenes for "Duet" where Cadman has control of McKay's body, Jamie Ray Newman would do a scene first, and then David Hewlett would try to mimic her movements, cadence, accent, etc. [1]
Alan C. Peterson, who played the Magistrate in "Condemned", previously played Canon in Stargate SG-1s Demons.
The episode title of "Trinity" is a reference to the Trinity test. [2]
The outdoors parts of "Instinct" were filmed on location at Lynn Valley Canyon, North Vancouver.[3]Jewel Staite, who played Kaylee Frye on the cult Sci-Fi show Firefly, is the second Firefly cast member to guest star on a Stargate series, the first being Adam Baldwin in Stargate SG-1 episode "Heroes". She would later go on to play Dr. Keller as a recurring guest star at the end of Season 3, continuing into Season 4 prior to becoming a series regular in season 5.
"Conversion" was actress Rachel Luttrell's first on-screen kissing scene.[4] Her parents were present for the kiss.[5]
Every scene in "Aurora" where Ronon appears in the environmental suit had to be played by a body double because Jason Momoa's head would not fit in the helmet.[6]
"Coup D'état" was supposed to feature the return of Acastus Kolya (last seen in "The Brotherhood"), but because of conflicts with Robert Davi's schedule it was rewritten to feature Kolya's second in command Ladon instead.
For "Allies", Brent Stait took over the role of Michael throughout the episode. Conner provided the voice after the crew felt it 'needed' it.[8]
"The Siege" received an Gemini nomination for "Best Visual Effects" in 2007.[9]
"The Hive" was nominated for a Gemini Award in the category "Best Sound in a Dramatic Series".)[10]
For "Grace Under Pressure", Joel Goldsmith was nominated for an Emmy in the category "Outstanding Music Composition for a Series (Original Dramatic Score)".)[10]
United States, 
Canada
