Todd informs the Atlantis expedition that a rogue group of Wraith has acquired several Zero Point Modules to power a formidable new Hive Ship, and wants it destroyed. However, after the Daedalus is disabled, they learn that the ship is heading straight for Earth, and they must stop it before it gets there.
Todd contacts Atlantis and reveals that a Wraith subordinate has mutinied and managed to use several Zero Point Modules, acquired during the destruction of Asuras, to power a formidable new Hive ship. He urges Richard Woolsey to attack and destroy it before it becomes a threat to Atlantis. On board the Daedalus, Colonel Steven Caldwell, Lt. Colonel John Sheppard and the rest of the team rush to engage the new Super-hive. But the vessel proves itself an impressive opponent, crippling the Daedalus before making a sudden and inexplicable jump into hyperspace.
Puzzled over the Wraith's sudden departure, Dr. Peter Kavanagh on board the Daedalus picks up a weak subspace signal in Wraith code. Dr. Rodney McKay is quick to recognize that the communique was sent, through subspace, from an alternate reality. Once deciphered, their worst fears are realized: the Wraith message contains a familiar set of coordinates — the hive ship is on its way to Earth. McKay is able to calculate where the hive ship will drop out of hyperspace before reaching Earth, of which they can notify Stargate Command via Atlantis once the communications array is repaired.
The team returns to Atlantis once the Daedalus' engines are repaired, but are dismayed to learn from a video transmission sent by Colonel Abraham Ellis that both Earth's starships, the Apollo and the new Sun Tzu, have failed miserably to stop the Wraith ship, with the Apollo, in bad shape herself, taking on crew from the crippled Sun Tzu. Sheppard interrogates Todd for the location of more ZPMs, which Major Evan Lorne and his team are able to locate; Atlantis, now with her full complement of three ZPMs, will return to Earth in a last-ditch effort to defend it. Sheppard expects to be the one flying the city, but he is informed by Woolsey that he will be returning to Earth. The task of flying the City ship then falls to Dr. Carson Beckett (much to the surprise and irritation of Dr. McKay.)
Beckett launches the city and Sheppard returns to Earth via the Stargate, alone, to command the chair from the Antarctic outpost at Major General Jack O'Neill's request. Back on Earth, Colonel Samantha Carter is temporarily in charge of Stargate Command, and Major Paul Davis informs Sheppard that the Wraith ship has arrived shockingly earlier than anticipated and is now on the other side of the moon, sitting still and doing nothing. They assume it is going to complete its integration with the ZPMs and then attack Earth. Sheppard is able to convince Carter and Davis to let him lead a squadron of F-302s refitted with Nuclear warheads, which are diverted to intercept Wraith Darts sent to destroy the Ancient Control chair (which had been relocated to Area 51), in advance of the main Wraith attack. The attack succeeds and with the chair destroyed, Earth is defenseless; Sheppard volunteers to go on a suicide mission to destroy the hive ship from the inside with the nuke onboard his F-302.
Meanwhile, International Oversight Advisory dignitaries prepare to escape Earth to the Alpha Site (Davis quips as "courageous to the end") but discovers the Wraith have overridden Earth's gate. At the very edge of the Milky Way galaxy, Atlantis' hyperdrive disengages due to overtaxing. Woolsey tries to dial Earth, only to find that it has dialed the hive ship above Earth — Ronon Dex, Teyla Emmagan, Lorne, and McKay enter the gate to infiltrate the hive ship. Meanwhile, Sheppard separately infiltrates the hive with his F-302 through the Dart bay, unbeknownst to the rest of the team. In a desperate battle on board the hive ship, Ronon is stabbed in a fight with two Wraith warriors. The knife has pierced his lung, and he dies from the resulting blood loss; with Teyla and McKay visibly upset, Lorne forces them to leave his body behind.
Back on Atlantis, with the hyperdrive out of commission, Dr. Radek Zelenka proposes activating a highly experimental and potentially dangerous Wormhole drive based on the same wormhole technology as the Stargate. With it, they could potentially reach Earth in seconds.
On the hive ship, just as Sheppard is about to activate his nuke, he receives a radio transmission from McKay who suggests activating it by remote, allowing the team to escape through the Stargate to the Alpha site. Sheppard and the team return for Ronon's body, only to discover the Wraith underling has revived Ronon for interrogation; the team kills the Wraith underling and his two guards and is able to rescue Ronon.
However, Sheppard and his team run out of time as they attempt to reach the gate and stopped in a corridor, Sheppard prepares to activate the nuke with all of them still on board. Thankfully, Atlantis arrives in position between the Hive and Earth to buy them more time. Atlantis takes the brunt of the hive ship's assault on Earth and launches a barrage of Drone weapons in retaliation. The sheer force of the Hive's weapons' fire is pushing the city ship into Earth's atmosphere, and it is straining the shields. With little power left, Beckett can either adjust the course of Atlantis, or keep firing at the enemy ship; Woolsey gives the order to keep firing. The team manages to escape to the Alpha Site, and the nuke successfully detonates, destroying the hive ship, but Atlantis is now forced to make a landing through Earth's atmosphere, risking burning up during re-entry.
Everyone at Stargate Command waits for news with bated breath, but erupts into celebration when Atlantis lands successfully over water. Although the re-entry caused a giant fireball across the sky, the city is able to cloak before landing, and the area in which they land, just past the Golden Gate Bridge on the Pacific Ocean side, is placed under naval quarantine, so for now at least, Earth's population is still in the dark.
Sheppard visits Todd, who's still locked in a holding room. Todd boasts about his help in saving Earth because of his ZPMs and asks if Sheppard has come to kill him, but Sheppard does not respond. Ronon is visited in his Atlantis infirmary bed by Sheppard when Amelia Banks walks in. She takes him to join the rest of the senior Atlantis staff on a balcony overlooking the Golden Gate Bridge in San Francisco.
McKay: Kavanagh. What the hell are you doing here?
Kavanagh: Reassignment. More fun and adventure in the Pegasus galaxy.
Todd: I may have acquired a few more than I let on.
Woolsey: How many more?
Todd: Let's not get caught up in unnecessary details.
Woolsey: I like… details.
Sheppard: The other ZPMs you talked to Woolsey about? Tell us where to get 'em, and maybe it'll improve your situation.
Todd: Am I supposed to be enticed by this offer?
Sheppard: No. I'll probably kill you anyway. But, don't forget, this Wraith betrayed you and got away with it. For no other reason, you might want to do it out of pure spite.
(Todd leans back, studying Sheppard.)
Todd: You...know how to talk to me, John Sheppard! (laughs).
(about Todd's credibility for the ZPMs)
Woolsey: He actually came through for us.
Sheppard: Maybe he's turning over a new leaf.
Woolsey: Get those down to Zelenka immediately.
Lorne: Yes, sir.
(Lorne starts to leave.)
Sheppard: Or maybe they're going to blow up when you plug them in.
Woolsey: (changing his mind) Have Doctor McKay check them first.
Sheppard: (to Todd) If I find out you're playing us, I'm not gonna wait for authorization. There isn't gonna be any paperwork. I'm just gonna kill you.
(McKay makes some final adjustments on a control panel.)
McKay: (into radio) All right. I've finished recalibration on the chair. Radek, how are things at your end?
Zelenka: (over radio) ZPMs are online and functioning one hundred percent. We're good to go.
McKay: Okay! Who's flying this puppy?
(Beckett quickly enters the room.)
Beckett: That would be me.
McKay: (confused) Carson?
McKay: What, they called you in for this?
McKay: You must have a higher CIA than I thought.
Beckett: Excuse me?
McKay: Chair Interface Aptitude. We have a... we have a ranking system.
Beckett: Well, apparently, after Colonel Sheppard, I'm number two.
McKay: (skeptical) Really? I'll have a look into that.
Woolsey: You're being asked to fly to another galaxy... to take - what might turn out to be the losing part - in a battle that isn't yours.
Ronon: You mean like everyone on this base has been doing for the past five years?
Teyla: Thank you for your consideration, Mr. Woolsey, but I assure you it is not necessary.
Ronon: We're not goin' anywhere.
Woolsey: (proudly) Very well.
(The Wraith underling revives Ronon and demand information about the rest of the team)
Wraith underling: Where are they?!
(The Wraith underling gets his answer as Sheppard and the others show up and kill him and his guards)
(The hive ship explodes in orbit of Earth)
Major Davis: They did it! The hive's been destroyed!
Carter: Atlantis this is Stargate Command, well done!
Woolsey: Thanks for the kind words, Colonel, but I wouldn't pop the champagne just yet. We've lost orbit, and Doctor Beckett is unable to compensate. We're goin' in!
Carter: Do you have enough shield to survive reentry?
Woolsey: We're about to find out.
Sheppard: Well, how you feeling?
Ronon: Ready to get out of here.
Sheppard: Take your time, the city's pretty banged up. Even with the ZPMs we're not going anywhere for a while.
Ronon: And when they fix it, you really think they're going to let us take it back to Pegasus?
Sheppard: I'll make sure you get home.
Ronon: This is my home.
Keller: (to McKay) You OK?
McKay: I'm alive. (Keller laughs) And I've got you, what else would I need?
Sheppard: Nice view.
Woolsey: Yes... yes it is.
- Joe Flanigan as Lt. Colonel John Sheppard
- Rachel Luttrell as Teyla Emmagan
- Jason Momoa as Ronon Dex
- Jewel Staite as Dr. Jennifer Keller
- Robert Picardo as Richard Woolsey
- David Hewlett as Dr. Rodney McKay
- Christopher Heyerdahl as Todd
- Mitch Pileggi as Colonel Steven Caldwell
- David Nykl as Dr. Radek Zelenka
- Kavan Smith as Major Evan Lorne
- Michael Beach as Colonel Abraham Ellis
- Martin Christopher as Major Kevin Marks
- Gary Jones as CMSgt. Walter Harriman
- Amanda Tapping as Colonel Samantha Carter
- Paul McGillion as Dr. Carson Beckett
- Colin Cunningham as Major Paul Davis
- Sharon Taylor as Amelia Banks
- Ben Cotton as Dr. Peter Kavanagh
- Tyler McClendon as Wraith underling
- Chuck Campbell as Chuck
- Jon Johnson as Parker (Uncredited)
- Eddy Huber as Coughlin (Uncredited)
- Tony Baretta as Smitty (Uncredited)
- D. Harlan Cutshall as Marine (Uncredited)
- David Neale as Technician (Uncredited)
- Bill Y.W. Butt as Doctor (Uncredited)
- Joshua Bazinet as SGC Tech (Uncredited)
- ? as Riggs (Voice)
- ? as Marine
- The transmission that the Super-hive receives from an alternate reality that gives it the location of Earth is the same one the Punk Wraith sent in "Vegas".
- Although it is not seen, this episode introduces a new Tau'ri ship, the Sun Tzu, a Chinese ship. It is the fifth Daedalus-class ship to enter service. The other four Deep Space Cruisers are the Daedalus, first seen in the Season 2 Stargate: Atlantis episode "The Siege, Part 3"; the Odyssey, first seen in the Season 9 Stargate SG-1 episode "Off the Grid"; the Korolev, first seen in the Season 9 SG-1 episode "Camelot"; and the Apollo, first seen in the season 3 Atlantis episode "First Strike". Another ship, the George Hammond is also mentioned. The George Hammond appears in both Stargate Universe and plays a major role in the Stargate Atlantis: Legacy series.
- Colonel Samantha Carter reveals to Lt. Colonel John Sheppard she is leaving Stargate Command to command the Phoenix, which has been renamed to George Hammond in honor of Lt. General George S. Hammond (in an homage to Don S. Davis, who died of heart failure on June 29, 2008). The ship would later be featured on Stargate Universe.
- In this episode, Dr. Beckett is the last person seen in an Ancient Control chair and he uses that chair to fire Drone weapons. In "Rising", the pilot episode, Dr. Carson Beckett is the first one seen in the chair, and his first act was to accidentally fire a drone. It is also revealed that he has the second best Control Interface Aptitude, after Sheppard. Dr. Rodney McKay is mildly annoyed by this and in "Rising", he was annoyed that he didn't have the Ancient Technology Activation gene.
- This is the second time that a Hive ship has entered hyperspace rather than continuing to fire on the Daedalus; a similar instance occurred in "Allies" when two regular Hives entered hyperspace just as the Daedalus planned to retreat. Those Hives also had left after learning of Earth's location.
- This episode marks the first appearance of Major Paul Davis since Stargate: Continuum and final appearance of Davis in the Stargate franchise.
- All three United States Air Force commanders of Stargate Command are mentioned, Major General Henry Landry who is heading a task force in Washington D.C., Major General Jack O'Neill recalling Sheppard and Lt. General George S. Hammond who has recently passed away. Coincidence or not, on top of this, this is also the last episode of the three current series to show Stargate Command, although the SGC does appear in a video in "Air, Part 1".
- Joseph Mallozzi confirmed in his blog that the Odyssey's secret mission is Icarus Base related, thus informally introducing Stargate Universe.
- This episode, along with the previous episode ("Vegas"), was leaked to the internet on December 22, 2008.
- At the end of the original airing of this episode on Sci Fi Channel, there is a brief trailer for Stargate Universe, saying that the first episode would premiere sometime in the Summer of 2009. However, the airdate was later moved to fall.
- This episode marks the only time Todd is addressed directly by that name, when Sheppard answers his radio call at the beginning of the episode. Curiously, he seems to know it is he being addressed. Presumably, he heard it mentioned at some point off-screen, possibly from Kenny, who heard McKay call him that in "The Queen".
- In this episode, another Hive ship is destroyed by Atlantis. This brings the total to 29 since the expedition arrived in the galaxy.
- In a tactic used often by the Goa'uld, the Wraith have a Stargate on board their ship to prevent Earth from dialing out. In this case as it's a Pegasus Gate it takes precedence over the Earth Gate as the dominant Gate to prevent Earth's gate from working at all.
- While its not shown in the aired version, the DVD version confirms that not only did the Iratus bug treatment work, but it reverted Todd to an ordinary Wraith again, not just cured his disease.
- This is the last episode in the Stargate franchise to feature the FN P90 Personal Defense Weapon.
- The events of this episode presumably occur over the course of several days to weeks as Colonel Steven Caldwell tells the team that it will take them days to weeks to repair the Daedalus hyperdrive. All that is shown is them discussing the plan to send the Apollo and the Sun Tzu after the Super-hive once the Daedalus communications are up again and then arriving at Atlantis a long enough time later for the Daedalus hyperdrive to have been repaired and the failed attack to have already occurred.
- References are made to the events of "McKay and Mrs. Miller", "Be All My Sins Remember'd", "Spoils of War", "The Daedalus Variations", "First Contact", "The Lost Tribe", "Infection" and "Vegas".
- Sheppard makes a reference to the alternate timeline of "The Last Man" when he asks if the new Daedalus-class battlecruiser will be called the Phoenix. This is the name the ship was given in that timeline.
- Colonel Samantha Carter, CMSgt. Walter Harriman and Major Kevin Marks all appear in the finales of both Stargate SG-1 and Stargate: Atlantis.
- Lt. Colonel John Sheppard, Dr. Rodney McKay and Teyla Emmagan are the only characters to appear in both the pilot and finale of Stargate: Atlantis (Dr. Carson Beckett technically appears in both the pilot and the finale as well, but this doesn't entirely count as the Beckett in the finale is a clone of the original).
- Christopher Heyerdahl appears in both the pilot and finale though as different characters; in the pilot he played Halling and in the finale he played Todd.
- Tyler McClendon (Wraith underling) previously played Lt. Adam Banks in the Stargate SG-1 episode "Avalon, Part 1", Wraith Commander (Broken Ties) in the Stargate: Atlantis episode "Broken Ties", Kenny in the episodes "The Queen", "First Contact" and "The Lost Tribe" and Wraith in "Outsiders".
- During the final battle over Earth and the shots of Atlantis flying through the atmosphere a new and entirely different CG model is used featuring no connected piers and whereas on the other CG models each pier looks slightly different this version has two sets of three identical piers.
- When Colonel Samantha Carter tells Lt. Colonel John Sheppard that they're renaming the Phoenix, she mistakenly says they're renaming it "the General Hammond", while the ship is actually named the George Hammond. It's possible she either intended to say it was named after General Hammond, or that they'll be naming it the George Hammond, but ship names do not tend to include the titles of their namesakes. In Stargate Universe and Stargate Atlantis: Legacy, the ship is called by its proper name, the George Hammond.
- When Atlantis dials Earth, the Stargate shield is clearly visible despite it being an outgoing wormhole when the Stargate engages. Moments later, there is no sign of the shield.
- When Sheppard returns to Earth, the Earth gates Event Horizon is textured as Atlantis, as both have different gate wormhole textures.
- The team goes on the most dangerous and most important mission yet and Dr. Rodney McKay only takes a M9 pistol instead of his usual FN P90 Personal Defense Weapon.
- The F-302 fighter-interceptor radio system would not operate (at least at default) on the same frequency as the short range radios of Atlantis Reconnaissance 1. Thus McKay and the team would not have heard Sheppard speaking to Stargate Command.
- The map of world borders seen on the left-hand side of the screen as Sheppard and Carter enter the Stargate Operations room appears to show Cold War era borders, indicated primarily by the split of Germany and the inclusion of the Soviet Union. This map would have thus been out-of-date for at least 18 years. In fact, this map would have been out-of-date prior to the construction of the Stargate Operations room itself.
- Won Leo for "Best Overall Sound in a Dramatic Series" (Kelly Cole, Patrick Ramsay, Bill Mellow, Joe Watts, Hugo DeLaCerda and Kevin Belen)
- Won Leo for "Best Sound Editing in a Dramatic Series" (Jay Cheetham, Steve Smith, Kirby Jinnah, Matthew Wilson and Jason Mauza)
- Nominated Gemini for "Best Visual Effects" (Mark Savela, Jason Gross, Paul Hegg, Brandon Hines, James Kawano, Alec McClymont, Krista McLean, James Rorick and Luke Vallee)
- French: L’Empire contre-attaque (The Empire Strikes Back)
- Hungarian: Ellenség a kapuknál (Enemy at the Gates)
- German: Feind in Sicht (Enemy in Sight)
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