Whilst O'Neill and Carter head to Washington to be decorated by the President and find a security leak, Jackson and Teal'c go to Abydos (after they unbury their stargate) to see Sha're's father. They arrive to tell him that they have been unsuccessful in finding Sha're, only to discover that she is already on Abydos. But they find that she is pregnant by Apophis and the baby holds the secrets of the Goa'uld.
General Hammond allows Daniel to revisit Abydos, as agreed within the year, accompanied by Teal'c. At arrival, Daniel sees quickly what escaped his wife Sha're's father Kasuf: she carries a goa'uld symbiont. In tears she admits to be pregnant and co-inhabited by Apophis's queen Amaumet, who remains dormant in order not to harm the child: the father is no lesser then the planet's former system-lord Apophis, who has evil plans. Finding she shares mentally, Teal'c insists they must take her to the star-base, as access to the genetic goa'uld memory is of immense strategic value against the evil race and Apophis wold only take the child forever; Kasuf agrees, so she accepts, but the approach of Heru'ur's ship -which she mistakes for Apophis's- makes Amaumet awake shortly. She gives birth to a son and Amaumet reemerges while their hiding is found by Heru'ur's men who capture only Daniel.. Meanwhile Jack and Sam go to Washington to receive presidential decorations. Sam is approached by her father, USAF General Jacob Carter, but must tell him she can't give up her present job -still classified, even for him- to accept the NASA space career he finally got her access to, believing it her life-dream. Next Jacob tells her he has terminal lymphoma cancer... Jack is meanwhile approached by journalist Armin Selig, who knows about the Stargate-program, even recorded Jack discussing it with Sam. O'Neil denies everything but is ordered to find out more about the leak. When they meet again and Selig clearly knows a lot, even about he attack on earth, Armin gets not only more denials but is fatally hit by a speeding car...
It's now been a year since Daniel Jackson left Abydos and although he has been unable to find Sha're, he feels he must return to tell her father what has been happening. With Jack O'Neill and Sam Carter in Washington to receive a medal from the President for their bravery during the Goa'uld attack, Daniel sets off with Teal'c only to find that Sha're is back on Abydos and very pregnant. Apophis has put her there for safekeeping and she is carrying his child who he intends to use as his own replacement when the time comes. Daniel is desperate to find a way to save her but realizes that any attempt to hide her or take her to Earth will result in retaliation from the Goa'uld god. In Washington meanwhile, O'Neill has an encounter with a reporter who seems to have acquired knowledge of the super secret Stargate project. As for Sam, she gets to see her father, Maj. General Jacob Carter who tells he's arranged to have her transferred to her 'dream' job.
Daniel informs the SG-1 that he must return to Abydos to tell to Sha're's father that he has not found her yet; otherwise the Stargate will be buried forever. Teal'c goes with him while Jack and Sam go to Washington to be decorated by the President. On the arrival, Daniel and Teal'c learn that Sha're is pregnant by Apophis and will deliver her baby in Abydos. Further, her Goa'uld is asleep to protect the baby, so Daniel is able to rekindle his love. Meanwhile Jack discovers that the secret about the Stargate has leaked to a snoopy reporter Armin Selig that blackmails him seeking confirmation.
- Keeping his promise, Daniel Jackson returns to Abydos a year after leaving, accompanied by Teal'c. There they find Sha're, seemingly free of the control of her symbiote, and nine months pregnant; the baby is Apophis', which he intends to use as his new host. Meanwhile, O'Neill and Carter head to Washington for a medal ceremony in their honor, discovering in the process that the SGC may have a serious leak. Back on Abydos, System Lord Heru'ur, an enemy of Apophis, comes to kidnap Sha're and her child. Daniel Jackson hides Sha're, who goes into premature labor, and Daniel delivers the baby himself. Sha're is taken over by her symbiote again after the birth, and Sha're/Amaunet returns with Apophis after she tells him that Heru'ur has taken their child, who Teal'c really leaves with Sha're's father on Abydos.