- This episode is part 2 of 2; it is preceded by "First Contact".
As Dr. Rodney McKay and Dr. Daniel Jackson are held prisoner by the Vanir, they make a startling discovery about who they really are. Meanwhile, "Todd" and his Wraith hijack the Daedalus to find and destroy those who activated the Attero device. The Travelers arrive and Lt. Colonel John Sheppard must help them get to the planet before "Todd" uncovers a way to destroy the device for good, even if it means sacrificing McKay and Jackson's lives to do so.
Previously on Stargate: Atlantis
Dr. Daniel Jackson arrived in Atlantis to find the hidden lab of the rogue Ancient scientist Janus, but this had attracted the attention of a group of aliens, who kidnapped Jackson and Dr. Rodney McKay and stole a device. Meanwhile, Todd and a delegation arrived on board the Daedalus to go forward with Dr. Jennifer Keller's gene therapy. However, Todd witnessed two Wraith cruisers getting destroyed the second they go into hyperspace. He accused the Atlantis expedition of getting hold of the Attero device. In anger, he stunned the crew and locked down the ship, as well as sending more Wraith to the ship. Jackson attempted to warn the aliens of a major flaw with the device; it would destroy any activating Stargate. In Atlantis, Lt. Colonel John Sheppard planned to rescue them and activates Atlantis' Stargate. However, the energy levels spike, causing the Gate to explode. Fortunately, they activated Atlantis' shield to cover the Stargate and to wait for the explosive energy to dissipate it until the threat is neutralized. However, the shield emitters started to overload. Sheppard ordered everyone but he and Dr. Radek Zelenka to evacuate from the central tower.
Teyla Emmagan goes down a few levels and tells everybody in that level to evacuate from the central control tower. Just as the expedition members evacuated, the city shook; the shield emitters overloaded, meaning that explosive energy created from the Stargate exploding was released, causing serious damage all around the top levels of the tower. Teyla and a group of medics, including Marie rush to Stargate Operations, where they find the entire room has been seriously damaged. Just as they think Lt. Colonel John Sheppard and Dr. Radek Zelenka were incinerated in the explosion, they hear groaning. They see Sheppard, who shielded Zelenka from the blast, and has shards of glass on his back. The two men are alive, having taken cover in the Conference Room.
Jackson and McKay have recovered from being stunned and are alone in a holding cell. McKay explains the side effect to Jackson. Wraith ships will be destroyed when they enter hyperspace. Ships on any other frequency, including those using Ancient technology, will be unaffected. But as long as the device is running, excess energy will build up in any Stargate that establishes a wormhole, eventually causing an enormous explosion (as happened to the Atlantis gate, although McKay and Jackson don't know that yet). Potentially millions of people throughout the Pegasus galaxy could be killed when their gates explode.
On board the Daedalus, "Todd" and his crew have just finished sending in all the Wraith troops and putting all the Humans into a Hangar Bay. He instructs the Hive Ship not to go into hyperspace, since the ship will be destroyed. "Todd" instructs his crew to send the Daedelus to Atlantis.
Back in Atlantis, the medics remove the glass from Sheppard, who tells the technicians and Zelenka to set up an Auxiliary control room, which they did quickly. When the medic is finished, he goes to the room, where it is mostly set up. They plan to contact the Daedalus, but before they can find a way, Amelia Banks finds that the Daedalus is contacting them.
The team is stunned to see that "Todd" has seized control of the ship, because he believes they are behind the activation of the Attero device. He thinks the negotiations were just a ploy to draw his Hive ship out into the open so the humans could see if the Attero device succeeded in destroying it. He has dropped the Daedalus out of hyperspace far enough away, so they are in communications range, but not near enough for Puddle Jumpers and Drone weapons to be sent to anytime soon. "Todd" says he is willing to let the crew and the Daedalus go, if they give him the location of the Attero device. He says he witnessed the weapon's effect 10,000 years ago during its first test, but the Lanteans shut it down when they realized it would destroy the Stargates. He believes Sheppard will use it because he known the Milky Way galaxy and Earth will be unaffected. He gives them a minute to give him the location, or he will feed on a crew member, one a minute, starting with Richard Woolsey.
The team in Atlantis quickly discuss their options. They know it is very likely that the signal from M6H-987 may have been the location of the device. But since there is a high chance Dr. Daniel Jackson and Dr. Rodney McKay are there as well, "Todd" may destroy everything in his path, including the two captives. They put "Todd" back on, and explains they are not behind this. Yesterday, a group of aliens infiltrated Atlantis and stole a device, which may have activated the Attero device. The Atlantis group decide they have no choice, millions of humans will die if the gates explode. They give Todd the coordinates to M6H-987. "Todd" then plots a course for the planet, and goes into hyperspace.
Elsewhere on the Daedalus, Ronon Dex and Dr. Jennifer Keller are still at large. Despite being in lockdown, Ronon manages to open a door, and kill two Wraith warriors. Ronon tells Keller that he knows how to sabotage the ship. They both head towards engineering.
In Atlantis, the expedition picks up a hyperspace window opening, but it is not "Todd"; they are the Travelers. The ship is captained by Katana Labrea, who was sent by Larrin. She enters Atlantis and tells them that they established a settlement on a planet for the first time in generations. However, the settlement was wiped out by the destroyed Stargate, which killed 3,000 people, and destroyed two ships, including their Aurora class vessel. She wonders why the Gates are exploding all over Pegasus. The team informs her about the Attero device and their stolen ship. Katana agrees to help them shut down the device. Sheppard and Zelenka board the ship to travel to M6H-987. Fortunately for them, Katana Labrea's ship is one of the fastest in the Traveler fleet. Sheppard leaves Teyla in charge.
In the Daedalus, Ronon and Keller arrive in engineering, where Ronon kills more Wraith. Keller wonders how Ronon will sabotage the ship. He opens the crystal tray on the Asgard computer core and shoots the control crystals, and shoots more on other areas, putting the ship's shields, weapons, and hyperdrive offline. The ship drops out of hyperspace. "Todd" accesses the ship-wide P.A. system and threatens to begin killing crew members unless Ronon and Keller turn themselves in. Ronon claims he's bluffing. However, Keller runs to another room and turns herself in. Ronon sighs and continues to look for weapons.
In Katana's ship, in the hopes of getting her ship's hyperdrive running at maximum output, Katana brings Zelenka and Sheppard into the aged and cluttered engineering room and introduces them to his chief engineer; Mila, who is only 15 years old. Mila has been working with the hyperdrive engine since she was four years old, and is a brilliant young woman who will do whatever is necessary to get the job done. Where Radek is cautious and doubtful that the job can get done (safely, at any rate), Mila shows him otherwise. However, he warns Sheppard that the system is cobbled together out of mismatched parts. It's possible that once they drop out of hyperspace, they won't be able to engage again. Sheppard tells him to just worry about getting there for now.
In Janus' outpost, Jackson is led into a room with another alien. He warns the aliens of the effect the device has on Stargates but the alien is unconcerned by the deaths of millions of humans. The alien explains that their planet can no longer sustain them, so for the first time in thousands of years they have to venture back out into the galaxy, which puts them in danger from the Wraith. They need the Attero device for their own survival.
Jackson demands to know who the aliens are inside their suits, knowing that they are not human. The back of the alien's suit opens and, to Jackson's astonishment, an Asgard steps out. An emotional Jackson informs them that the Tau'ri have encountered the Asgard before and were even allies with them along with friends. After Jackson informs him that all the Asgard in the Milky Way committed suicide because of genetic degradation from cloning the Asgard tells him that the Asgard in Pegasus are also clones but by continuing Loki's research on humans they are fixing the problem. They believe in Loki's philosophy that the ends justify the means. 10,000 years ago, they fled to the Pegasus Galaxy to experiment on the humans there, counting on the Ancients to win the war.
For a time the Ancients and the Wraith were too busy fighting each other to notice what the renegade Asgard were up to, and they made progress in their research. But they had assumed the Ancients would win the war. When the Wraith won, they knew they were in danger because the Wraith destroy any civilization with advanced technology. They lost their intergalactic ships in the first Wraith attack, and were forced to retreat to a planet with a toxic atmosphere. That's why they wear the protective suits. But the planet ultimately become unlivable, even with their technology. They left, and came to Janus' lab.
After a brief interrogation by "Todd", in which he tells her about Sheppard's cooperation in the mission to destroy the Attero device and save hundreds of thousands of human lives, a skeptical Keller is escorted to the room where the rest of the Daedalus crew is being held. Before they can get there, Ronon drops from the ceiling and kills the two Wraith holding Keller. Ronon hands her a FN P90 Personal Defense Weapon and they both kill more Wraith. Soon, the ship's hyperdrive are online, but the ship's weapons are damaged beyond repair. "Todd" tells the Wraith not to worry, since he has another idea. Ronon finds the crew and releases them. They need to get to the armory and retake the ship.
On M6H-987, Jackson returns to the room McKay is in. He tells McKay that the aliens are Asgard, which he finds surprising. They need to figure out a way to stop the device. McKay is able to manipulate the door controls into opening, and they escape. As they enter another room, they see more suits. McKay pleads for their lives, but Jackson notices that the two suits are empty. They have an adaptive interior that makes them "one size fits all."
This presents them with an opportunity. Meanwhile, Katana's ship arrives over the ice planet with Sheppard flying and sees no sign of the Daedalus, but notices three spaceships zeroing in on them. They prepare for battle. Sheppard daringly goes close up to one and Katana uses the ship's weapons to destroy a ship.
On the Daedalus, the armed crew storm the bridge, without encountering a single Wraith. There is no one in the bridge. The crew quickly finds out that they are also locked out of the ship's controls and the Daedalus is on a course to Janus' lab. A life sign scan reveals that all the Wraith are aboard their scout ship in the F-302 fighter-interceptor bay. The crew try to regain control, but are unable.
In Janus' lab, McKay and Jackson (in suits) stun the Asgard guards so they can shut down the device. However, there is a problem; turning the device off requires the control key, which was taken by the Asgard leader who is on one of the ships. The only option left is to get into the device room to remove a crystal. They have to face harsh radiation and electrical currents. Fortunately, with the suits, they can survive the radiation, but maybe not the currents. They both plan to walk in.
The Daedalus arrives above the planet to find the Traveler ship engaged in battle with the Asgard ships. "Todd's" ship exits the 302 bay and disappears. The Traveler ship makes contact with the Daedalus to ask for help and are surprised to find Woolsey and the crew in control of the ship. They quickly discover that "Todd" has programmed a command sub-routine on the ship to a collision course with the lab in order to destroy it and the Attero Device. The crew relies on Major Kevin Marks to retake control as the ship dangerously enters the atmosphere. However, As the Daedalus speeds through re-entry and is about to collide with the lab, the Traveler ship opens a hyperspace window in front of the Daedalus and both of them enter it seconds before the Daedalus impacts the planet, carrying them to the other side of the planet. Marks then succeeds in regaining control of the ship and the Traveler ship destroys one of the other Asgard ships they find there. The last one flees into hyperspace during the battle.
McKay and Jackson enter the room to remove the correct crystal, or the antenna will explode, killing them all--but they aren't sure which one to remove. Through the heads up display, McKay identifies the right crystal. However, as he does, Jackson gets hit by an energy strike, severely wounding him. As the two men are contemplating their deaths, they are beamed aboard the Daedalus and Jackson is taken to the Medical bay. McKay tells Woolsey that the device is inactive, and unless they take back the crystal McKay took, the device will not activate again. However, this is not enough for Woolsey who wants to ensure the Attero device will never be used again. As the Daedalus weapons are still down, he contacts Sheppard and orders him to destroy the Attero device. Sheppard fires on Janus' outpost with the Traveler ship's weapons, destroying it and the Attero device. They return to Atlantis.
Back on Atlantis, the team begins repairs on the city and the Daedalus. The Atlantis expedition has salvaged one of the Spacegates from the former McKay/Carter Intergalactic Gate Bridge to use as their new gate. Ronon asks Keller out to get some food. However, she tells him that it was good for him to come, since they'd be all dead if he wasn't, but tells him that she is interested in someone else. Ronon hides the fact that he is interested in her, albeit hiding it badly. McKay visits Jackson in the infirmary, where he tells him that Major General Henry Landry feels that he should be sent back to Earth to properly recover from his injuries.
Sheppard: Five bucks to anybody who can figure out how to contact the Daedalus.
Banks: (her console beeps) Uh, Colonel Sheppard?
Sheppard: Got an idea, Banks?
Banks: Well, no, but I am being hailed by the Daedalus on subspace. Does that count?
Sheppard: Technically that's not your idea, but good enough. Put ‘em on screen. I'll pay you later.
Todd: Transmit the coordinates or I will feed on Mr. Woolsey before your eyes.
McKay: You okay? I thought you were a goner!
Jackson: I'm alright.
McKay: I mean, they need ME. You're kind of expandable. I just figured they...
Jackson: Yeah, I got what you meant by 'goner'. Thank you.
McKay: Well, what did they want?
Jackson: Uh, to talk, actually.
McKay: Oh. Well. How did that go?
Jackson: They're Asgard.
McKay: For real?
Jackson: Yeah. A faction that broke off from the guys we knew thousands of years ago. They're the ones inside the suits.
McKay: I did not see that one coming...
Jackson: Apparently no fans of the Wraith, either.
McKay: Well, are they gonna shut off the device?
Jackson: Um... No.
McKay: Then I don't care. I mean, as long as that device is on, then millions of people could die. Besides, I think I've figured a way out of here.
McKay: This, is an Ancient facility, and Rodney McKay knows a thing or two about Ancient facilities.
Jackson: You know, it has been clinically proven that referring to yourself in the third person is a sign of mental instability, right?
McKay: Mentally unstable like a fox.
(door opens revealing two Asgard suits)
McKay: (pleading) Oh my God, please don't kill me, you need me.
McKay: Us, us. You need us. Look, the device needs constant care. I mean, true, I'm the only one who knows how to work it. You don't have to kill me for it, you're not a violent race. I mean, you may have stunned us a few more times than I would have liked, but who's to say we didn't deserve it.
Jackson: Rodney, they're just suits-
McKay: Yeah, suits. Suits that house one of the smartest races that ever evolved. The Asgards, I've always been a big fan of the Asgards. Some of my best friends are Asgards.
Jackson: They're empty suits. (waves his hand in front of their helmets) See?
McKay: (defeated) I know I was uh...
Jackson: You were...?
McKay: Yeah, it's not important..
McKay: (referring to the impending hazardous mission) Y'know, we don't both have to go in there.
Jackson: Well, when you get killed by one of those discharges, someone's gonna have to finish the job, so... (shrugs)
McKay: Good pep talk.
McKay: (referring to the electric discharges) I'm pretty sure we want to avoid those touching us.
Jackson: Thanks, Coach!
Sheppard: I just opened up a hyperspace window big enough for the both of us. We just traveled through the planet.
Marks: (to Woolsey) I got it. I'm back in. We've got control of the ship.
Woolsey: And not a moment...too late.
Woolsey: That's a new look for you.
McKay: Well, you know me, function over fashion.
McKay: (wearing armor) You wanna...unzip me?
Woolsey: I'll look for a can opener.
Jackson: So you can only give compliments to the dying?!
McKay: It's something I'm working on.
- 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
- Michael Shanks as Dr. Daniel Jackson
- David Nykl as Dr. Radek Zelenka
- Christopher Heyerdahl as "Todd"
- Daniella Alonso as Katana Labrea
- Martin Christopher as Major Kevin Marks
- Tyler McClendon as "Kenny"
- Sharon Taylor as Amelia Banks
- Claire Robertson as Mila
- Linda Ko as Marie
- James Chutter as Male Wraith
- Chuck Campbell as Chuck (Uncredited)
- Colin Corrigan as Lt. Rivers (Uncredited)
- Hector Navarro as Ramirez (Uncredited)
- D. Harlan Cutshall as Marine (Uncredited)
- Craig Fraser as Marine (Uncredited)
- Shaker Paleja as Doctor (Uncredited)
- Bill Y.W. Butt as Doctor (Uncredited)
- Lalo Espejo as Scientist (Uncredited)
- ? as Vanir leader
- ? as Vanir 1
- ? as Vanir 2
- ? as Vanir 4
- David Hewlett (Dr. Rodney McKay) announces the "Previously on Stargate: Atlantis" in the beginning of the episode.
- Todd is at least 10,000 years old, as he says he was there when the Attero device was first activated after Janus had built it.
- When the Daedalus' hyperdrive is repaired and Todd takes her into hyperspace, the same footage of the Daedalus entering hyperspace at the end of "Midway" is used, only sped up.
- The traveler ship's engine room is reminiscent of Serenity and Mila seems very much like Kaywinnet Lee Frye from Firefly.
- The Vanir that Dr. Daniel Jackson talks to has a 4-pip rank insignia. This may be a reference to Star Trek (TNG/DS9/VOY era) where such an insignia denotes the rank of Captain (4 pips only) or Admiral (4 pips enclosed in a rectangle). This Vanir is likely the leader of his people, much like Thor was the Supreme Commander of the Asgard fleet.
- The idea of sending the Daedalus through M6H-987 is similar to the Stargate SG-1 episode "Fail Safe", in which SG-1 saves Earth from a naquadah asteroid by sending it into hyperspace through Earth.
- It should be noted that the Vanir ships are not as advanced as their counterparts in the Ida galaxy, since a lone Travelers' ship is able to take out two without too much difficulty, though they make a point of saying their more advanced intergalactic ships were destroyed by the Wraith. Given their lack of resources, it is likely they simply did not have the resources to build better ships. Stargate Atlantis: The Third Path reveals that the Vanir have an old Asgard scoutship that's still capable of intergalactic hyperspace travel, but is likely unsuited for combat.
- A video leaked from Sci Fi Channel to YouTube before the episode aired showed that the aliens were in fact a renegade Asgard faction.
- Spoilers: The Vanir, the rogue Asgard faction return in Stargate Atlantis: Unascended and Stargate Atlantis: The Third Path. There they chase after Dr. Elizabeth Weir who had briefly Ascended and then been returned to human form by the Ascended Asgard Ran. Their hope was to use Weir to find Ran and force her to descend in hopes of using her uncorrupted genetic material to save their race. With the help of Weir, the team negotiates an alternate solution: contact Ran directly and ask her for help instead of forcing it upon her. Ran agrees to help and descends to aid the Vanir. Afterwards, the Vanir promise to leave everyone else alone.
- According to director Andy Mikita, the Heads up display inside the Armored exoskeleton was inspired by the similar suit display in the movie, Iron Man, which was released five months prior to the airing of this episode.
- This episode marks the final appearance of Dr. Daniel Jackson (Michael Shanks) on Stargate: Atlantis.
- Though Chuck appears in the episode, he has no lines, merely working in the background of the Auxiliary control center.
- James Chutter (Male Wraith) previously played Babbis in the Stargate: Atlantis episode "The Return, Part 1", Wraith scientist in "Midway" and Billy in "The Queen" and "First Contact".
- When they locate the Wraith on the Wraith scout ship, the ship is in the opposite landing bay in which it arrived. Whether it was moved on purpose or was an error is unclear. It also came into the landing bay nose first, but on the screen is shown parked nose-out.
- For the majority of the episode, Dr. Jennifer Keller appears to have wavy hair. However, when Todd is threatening her as she takes the blame for destroying the Daedalus' hyperdrive, her hair is straight. Two scenes later, her hair is wavy again.
- When Dr. Rodney McKay and Dr. Daniel Jackson make their escape they encounter two empty Vanir suits. During the conversation the camera appears over the shoulder of the "empty" suits, but some slight and unavoidable motion by the actors in the suits is visible.
- Despite appearing in the previous episode, Colonel Steven Caldwell is not seen aboard the Daedalus when the ship is retaken. He is later shown to still be around during "Enemy at the Gate", confirming he wasn't taken by the Wraith or killed. No explanation is given for his absence with Richard Woolsey and Major Kevin Marks appearing to be the ranking members of the Daedalus crew.
- Hungarian: Az elveszett törzs (The Lost Tribe)
- German: Der verlorene Stamm (The lost Tribe)
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