Five airmen are playing cards in an underground bunker beneath Cheyenne Mountain, Colorado. They're in charge of watching a single item: a large cloth-covered disc. When the one female airmen wonders what happens if their superiors catch them playing cards, the others assure her that nobody ever comes down there. They're interrupted when the cloth over the disc starts to move on its own. As the female airman goes to check it out, a sudden wind rips the cloth off… the Stargate. The entire chamber starts to vibrate as the Stargate activates on its own. An incoming wormhole opens and a metal sphere bounces through. The female airman picks it up and a scanning ray surveys the chamber. A warrior in serpent-styled armor come through the gate and grabs her, forcing her to drop her gun. Other Serpent Warriors come through, lead by a figure in imperial gold Serpent armor. The leader has his lead warrior, First Prime Teal'c, give him the airman who he scans with a hand device. He stuns her and the other airmen open fire. The Jaffa warriors have bulletproof armor and return fire with staff blasters. The airmen manage to kill two of the Jaffa but are killed themselves. The last one manages to send an alert before dying. Base commander General George S. Hammond leads a team of men to the chamber but orders them to hold their fire because of the female airman held hostage. The leader removes his helmet to reveal an Egyptian figure with glowing eyes. He glares at Hammond for a moment, and then he and Teal'c depart with the woman, shutting the Stargate down behind them.
Major Bert Samuels and two soldiers drive to a log cabin to talk to the owner: former Air Force Colonel Jack O'Neill. Jack is up on the roof watching the stars. Samuels climbs up and tells him that Jack is being recalled to Stargate Command to meet with General Hammond. Jack reluctantly goes along and meets with Hammond, who shows him the body of one of the intruders. The alien humanoid has a marsupial-like pouch in his stomach but nothing inside. Jack recognizes the staff weapons from when he went to Abydos but notes that all the people there were humans except for Ra. Hammond wonders if the leader he saw was Ra but Jack says he couldn't have survived the nuclear device they set off.
Hammond recalls Kawalsky and Ferretti, the other two survivors of the Abydos mission, then asks Jack about Daniel Jackson. Jack admits that Daniel helped them on the mission despite his civilian status, saying the scientist died setting off the nuclear device after Ra captured it. To be on the safe side, Hammond prepares to send another nuclear warhead through the Stargate to Abydos and Jack is forced to admit that he lied: they left Daniel with the Abydonians and instructions to bury the Stargate. Angry that Jack disobeyed orders, Hammond orders him confined with Kawalsky and prepares to send the warhead through anyway. Kawalsky and Jack compare notes, and Jack notes that he broke up with his wife and still isn't over the death of his son. Jack is thinking about Skaara, the Abydonian boy that befriended Jack. They're interrupted when Hammond comes in. He's reconsidered his decision having found out about the innocents, and wants to send a probe through. Jack has a better idea: remembering Daniel's allergies, he tosses a box of Kleenex into the wormhole. A few hours later the Stargate reactivates and someone tosses the Kleenex back with a message of thanks written on it. Hammond reactivates Jack and gets the authorization to send a team to Abydos.
Jack, Kawalsky, Ferretti, and a new team of men assemble for a meeting the next day and Hammond tells them that a Sam Carter will be joining the team. Sam arrives and it turns out she's a woman and a scientist. Jack is skeptical despite the fact she fought in the Gulf War as a pilot. Samuels suggests they simply bury the Stargate but Jack warns that Ra had ships and can visit them, and the Stargate is the only way they have to gain intelligence on the new invaders. Hammond tells them they have 24 hours to make contact with Daniel on Abydos and send a message, or he'll send the warhead through.
Jack and the others arrive on Abydos in the underground chamber. Several Abydonian boys with the guns Jack's first team left ambush them but Daniel shows up and calms everyone does. Skaara, one of the boys, hugs Jack in greeting. Daniel introduces them to his wife, Sha're. The chamber holds a dialing device, the one that the Stargate on Earth lacked. Jack brings Daniel up to speed but Daniel assures him that Ra is dead and no one has used their Stargate.
They share a meal with the Abydos community and Daniel talks about how he met Sha're. Skaara returns Jack's lighter while Daniel concludes the invaders have another Stargate and came from a different planet. Leaving Ferretti and the rest of the team behind, Daniel takes Jack, Sam, and Kawalsky to a nearby pyramid with a chamber containing galactic charts showing a network of Stargates. Working together, Sam and Daniel figure out that the symbols are out of date due to 50,000 years of galactic drift. Earth and Abydos are close enough that their coordinates remained valid. Sam figures they can adjust the coordinates compensating for the time shift, but unfortunately the aliens could have come from anywhere.
Ferretti and the others are waiting when the Stargate opens and the golden-armored leader and Teal'c arrive with a squad of Jaffa. Their firearms are no match for the armored Jaffa and their blasters. Ferretti is badly injured and the other soldiers killed along with the Abydonian boys. Teal'c spots Sha're and takes her captive along with Skaara when the boy tries to defend Daniel's wife. The leader scans Skaara and, declaring him perfect, knocks him unconscious. He then admires Sha're and says that she is the one he has been looking for. The leader dials coordinates into the Stargate and departs with his Jaffa and prisoners, unaware that the wounded Ferretti managed to see the coordinates.
Daniel and the others return and question the survivors, who insist that Ra has returned. Daniel is angry at himself for removing the capstone on the Stargate and allowing the invaders access. Jack tells Daniel that he's coming back to Earth with them, and they can find Sha're and Skaara together. Daniel tells the remaining Abydonians that they should bury the Stargate for a year, and he'll notify them then if he has found Sha're. Otherwise they should bury the Stargate for good. The Abydonians bid Daniel farewell as he returns with Jack and the others to Earth.
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