As the Gate Room blows up, Teyla tries to contact Sheppard and the medical teams move in. They hear a groaning noise and find Sheppard and Zelenka have survived.
Todd secures his hold on the Daedalus and sends out a message to warn the other Hive ships not to activate their hyperdrives… then orders a course for Atlantis.
McKay tries to work out how the Janus Device overloads Stargates and millions will die if they don't shut it down.
Woolsey wakes up and Todd has him brought to the control room to witness their attack on Atlantis.
The Atlantis teams have rerouted control when the Daedalus arrives and Todd hails them. Todd offers to return the ship and crew in return for the Attero Device. Sheppard has no idea what he's talking about and Todd explains that he was there ten thousands years ago when the Ancients shut down the device rather than risk the side effects. Todd threatens to start kill members of the crew, starting with Woolsey, until Sheppard tells him what he wants to know. Sheppard and the others figure that McKay and Daniel are at the Attero Device's location and the Stargate side effects are unintentional. Sheppard reestablishes contact and informs Todd they're not the ones behind it, but they know where the Attero Device is. Sheppard offers to take them there but Todd refuses to let him board, and demands the coordinates. Sheppard gives in and Todd informs him they'll be in touch.
Ronon tries to pull apart the airtight bulkheads without success while Keller looks on. The doors open and two Wraith soldiers open fire. Ronon shoots them down and heads for an access ladder to engineering to cripple the ship.
A hyperspace window opens near Atlantis and Katana, a Traveler representing Larrin, asks them why Stargates are blowing up.
The suited aliens take Daniel with them at gunpoint and McKay wishes him good luck.
Katana lands and explains that their first colony was destroyed when its Stargate blew up. She offers her ship and Sheppard and Zelenka go with her to track down Janus' lab while Teyla remains in command of Atlantis.
Ronon takes out the Wraith in engineering and then shoots the controls. The Daedalus comes out of hyperspace and Todd orders troops down to the engineering room. Ronon continues to shoot the vital systems until Keller persuades him to stop.
Daniel is brought before the aliens' leader and he tries to convince him to shut down the device. Since they don't use the Stargates, they are unconcerned about the Janus Device's side effects. It explains their planet is dying and the must destroy the Wraith before they venture out into the Pegasus Galaxy.
Katana shows Sheppard and Zelenka her modified engineering room and boasts that they can outrun most ships. She introduces them to her chief engineer, Mila, who is 15 years old. Sheppard has Zelenka assist her in increasing the ship's speed.
Todd has his men begin repairs and orders Ronon and Keller to surrender over the loudspeaker within three minutes or he'll kill the crew. Keller tries to surrender to buy them time, but Ronon refuses to let her do so. As soon as Ronon's back is turned, she runs off to surrender.
Daniel tries to get through to the alien leader and wonders why they're still in their battle armor. It opens its suit to reveal that it's an… Asgard. Daniel explains that he worked with the Asgard who were clones who suffered cellular degradation. The Asgard leader explains that they conducted human research to perfect the cloning process.
Zelenka informs Sheppard that Mila's engines may malfunction once they drop out of Hyperspace. When the radiation sensors start going off, Sheppard heads back to the bridge.
The Asgard leader explains that upon coming to the Pegasus Galaxy, they lost their intergalactic ships in the first battle and went to a planet with a toxic atmosphere. The planet's atmosphere grew increasingly lethal and they were finally forced to leave the planet. It insists that with their brothers dead, they have to fight to survive or the last remnant of Asgard civilization will be wiped out of existence.
Keller is brought before Todd, who wonders where the weapon she used to destroy the controls are. She claims to have ditched it and Todd claims that he's on a mission on behalf of Sheppard, and her sabotage has put the mission at risk. The hyperdrive come back on-line but the weapons are permanently non-functional. He assures her they'll figure a way to complete their mission and imprisons her with the other captured crew.
Daniel is returned to the cell with McKay and he explains what he learned from the Asgard. McKay has figured out a way to submit: he triggers the equivalent of a fire alarm to open the doors and they go to shut down Janus' device.
As Wraith soldiers take Keller to her cell, Ronon ambushes them. They free the prisoners and head for the armory to get weapons and take the ship back.
McKay and Daniel stumble across two empty Asgard suits, and Daniel notes the insides change to fit the owner.
Sheppard helps take the controls and the Traveler ship emerges from hyperspace above the Asgard planet. The hyperdrive burns out just as Zelenka predicted. Two Asgard ships close in and Sheppard pilots the Traveler ship through evasive maneuvers.
Ronon and the others take the bridge and discover that the Wraiths have retreated to their ship in the landing bay. Ronon goes to investigate while the others discover the controls are locked.
Daniel and McKay enter the control room and take out the Agards, but McKay discovers that they need a control key to shut down Janus' device. The remaining Asgard depart the base in their spaceship.
The Travelers take out one Asgard ship but a third one from the planet arrives and then enters hyperspace. Another hyperspace window opens further out and the Daedalus emerges. Woolsey makes contact and then learns that a subroutine program has kicked in and locked the guidance device to send the Daedalus on a collision course for the Asgard base.
With time running out, McKay suggests they keep the suits on and go into the crystal chamber. The suits should protect them from the radiation and electricity while they pull the power crystals out.
Todd and his people leave the Daedalus while McKay and Daniel enter the power chamber. McKay has to pull the correct crystal or the transmitter will explode. In orbit, Sheppard tells Mira and Zelenka to open up they hyperdrive in 30 seconds. The Daedalus enters the atmosphere… and the Traveler ship pulls ahead of them and opens a hyperspace window which they both pass through to the other side of the planet.
Daniel takes a blast of electricity and collapses, and McKay completes removal of the power crystals. In orbit, Marks regains control of the Daedalus and the two ships open fire on the remaining Asgard cruisers.
Daniel says he's pretty busted up and won't last much longer. McKay starts to say he respects Daniel… and they're beamed up to the Daedalus. Woolsey orders Sheppard to destroy the base and the Attero Device.
Back on Atlantis, Katana informs Sheppard they'll be building a new settlement and assures him they'll be in touch. Ronon invites Keller to dinner and she thanks him for coming on the mission, but informs him that she's interested in somebody else. Ronon passes it off and informs her she was wrong about thinking he had any feelings for her. However, he passes on the dinner off.
McKay visits Daniel in the infirmary and explains he's proofed their shields against Asgard incursion. Daniel is being sent back to Earth for medical recovery and they have gotten a Stargate from the bridge system, so he'll be heading back shortly. He thanks McKay for saying he respected him, but McKay points out he didn't finish the sentence and would have said "regret," not respect." Daniel wonders if McKay can only compliment the dying, and McKay admits that he's working on it.