Colonel Jack O'Neill retired from the military a year ago. Prior to retirement, he led an expedition through the Stargate, an ancient portal which allows instantanous travel to other galaxies. He is called back to duty by General Hammond when a group of aliens emerge from the Stargate, kill the soldiers guarding it and kidnap a female guard. After seeing the aftermath of the alien attack and the strange bodies they left behind, O'Neill confesses that he defied the order to destroy Abydos, the world he visited via the Stargate. He reveals that Daniel Jackson, the scientist who was thought to have died on that mission, is alive and living on Abydos. It is also clear that these aliens are not from Abydos.
O'Neill is reunited with his old comrades Kawalsky and Ferretti and joined by Capt. Samantha Carter, an astrophysicist. SG-1 returns through the Stargate to Abydos. They discover that Jackson has taken an Abydan wife, the beautiful Sha're, and that Skaara, the young Abydan boy O'Neill cherishes as a son, has grown into a fine young man. They also see Jackson's latest discovery: a giant cartouche covered in hieroglyphics that seems to be a map of many Stargates throughout the galaxy.
As they marvel, however, the aliens led by the handsome but evil Apophis, are making use of a similar map. They emerge from the Stargate on Abydos, and after a brief battle, kidnap Sha're and Skaara. Ferretti, who was wounded in the fire fight with the aliens, has seen the hieroglyphic code that indicates the alien's destination. O'Neill and Jackson are determined to follow the aliens and to save their loved ones