Daniel returns to Abydos on the first anniversary of his departure and is shocked to find Sha're in the care of her father, temporarily in control of her body and nine months pregnant with the child of Apophis. Meanwhile, O'Neill and Carter attend a medal presentation in Washington, where Carter runs into her estranged father and O'Neill meets a reporter who knows a little too much about the stargate program.
First appearance of Jacob Carter.
"Secrets" provides examples of the following tropes:
- Always Save the Girl: Daniel is far more concerned with the fate of his wife than the fate of his planet.Teal'c: The knowledge she possesses could one day save your world.
Daniel: I don't care!
- Awesome Moment of Crowning: O'Neill and Carter are both awarded medals for their part in stopping the attack on earth during the season opener, presented by General Hammond in the briefing room when the President is unable to make it in person.
- Blatant Lies: The official cover story for the stargate program is apparently 'Deep Space Radar Telemetry', something that Jacob Carter has a hard time buying. When caught on tape talking about "travelling halfway across the galaxy without getting lost" by the Intrepid Reporter, O'Neill also claims that he was referring to a class of airplane called the 'Galaxy' .
- Chekhov's Skill: Daniel's midwifery skills once again become relevant when Sha're goes into a labor as they are hiding from Heru'ur's forces.
- Child by Rape: Sha're's baby is the product of Apophis and Amaunet having sex via their host bodies, something that neither host had a say in.
- Clean, Pretty Childbirth: Played ridiculously straight; after an impressively short labor Sha're/Amaunet is left perfectly clean, if a little sweaty and disheveled, while Daniel wraps the equally-clean baby in a sheet he seems to have plucked from thin air. By the time Amaunet reunites with Apophis at the end of the episode, she is once again in full make-up and looking no worse for wear.
- Sha're's condition at the end is justified by Sha're being the host of a Goa'uld, which is specifically stated to give the host a Healing Factor. This does not justify the lack of mess though.
- Cool, but Inefficient: Heru'ur's personal shield, which deflects bullets and energy blasts but it's penetrable by slow-moving objects such as a thrown knife.
- Delivery Guy: Daniel is forced to deliver Sha're's baby when she goes into labor earlier than expected.
- Doctor, Doctor, Doctor: When O'Neill excuses himself from a conversation with the Carters and General Hammond:O'Neill: General. Captain. General... Waiter!
- Double Standard: Rape, Sci-Fi: Averted; Sha're is deeply ashamed of being impregnated by Apophis against her will and worried that Daniel will hate her, while Daniel is horrified by the whole situation but remains one hundred percent devoted to Sha're.Sha're: Do you hate me?
Daniel: No. No, I love you... I hate what's been done to you.
- Dramatic Irony: Jacob is upset when Sam doesn't seem interested in his offer to get her into NASA as it's always been her dream to be an astronaut and he can't understand why she would give that up. The irony is that she's already going into space, much further out than she would ever be able to with NASA, but she can't tell him about it because the stargate program is classified and Jacob has no need-to-know.
- Dressing as the Enemy: Teal'c dons the armor of a Heru'ur guard in order to steal the newborn baby from Amaunet who had just given birth to her, telling her to let Apophis know Heru'ur took the child. Still in the armor, he informs Heru-ur that Apophis successfully retrieved the baby. Conveniently, he also had the chance to kill Heru'ur's guards when O'Neill and Carter arrive through the stargate in the same uniform.
- Easily Forgiven: Sha're doesn't seem to bear any grudges against Teal'c for picking her out as a host in the first place.
- Exact Words: When Daniel thought about taking his wife's child with him, he tells his father-in-law Kasuf to tell Apophis that an enemy of Apophis stole his child. Since Heru'ur was there to steal the child, Apophis could be free to believe that.
- Fighting from the Inside: Sha're is shown to be fighting against Amaunet's control when the latter briefly surfaces as she goes into labor. At the end of the episode, when Amaunet has once again taken control, she looks directly at Daniel while the team is hiding from Apophis but does not give away his position; it's left ambiguous whether this is due to Sha're's influence or not.
- Idiot Ball: O'Neill and Carter openly discussing the stargate program in a public place, in broad daylight, possibly isn't the smartest move.
- Intrepid Reporter: Armin Selig. It doesn't end well for him.
- It's All About Me: Teal'c accuses Daniel of wallowing in his own self-pity rather than being there for his wife when they first find Sha're on Abydos. He does kind of have a point, and Daniel gets his act together after this.
- Killed to Uphold the Masquerade: Maybe. O'Neill certainly suspects this is the case when Selig is killed in a hit-and-run. Hammond assures him it was an accident, but even if the Air Force isn't responsible, there are definitely shadier organizations that could be involved. Either way, the audience never finds out for certain.
- Leaning on the Fourth Wall: Jack's Spell My Name with an "S" comment below is the show poking fun at the Stargate movie, which had a relatively un-funny Jack O'Neil, one 'l'.
- Living MacGuffin: Sha're's newborn son, who Apophis apparently intends to make into his next host, is consequently being hunted down by the forces of both Apophis and Heru'ur.
- Look Both Ways: Armin Selig is killed by a speeding car after stepping out into the road in the middle of a conversation with O'Neill.
- Military Brat: It's revealed that Sam Carter is the daughter of Air Force General Jacob Carter.
- Neuro-Vault: Sha're has access to the Goa'uld Genetic Memory while Amaunet is dormant inside her.
- Nice Job Fixing It, Villain!: Heru'ur's forces showing up on Abydos makes it relatively easy for Daniel and Teal'c to trick Amaunet - and consequently, Apophis - into thinking it was Heru'ur who took the child, effectively sending Apophis on a wild goose chase and leading his suspicions away from Kasuf and the Abydonians.
- Pre Asskicking Oneliner:Heru'ur: You dare challenge me?
O'Neill: I was thinking about it. [throws knife]
- Real Award, Fictional Character: Jack and Sam are awarded the Air Medal, a major Air Force decoration, officially for their work in "deep-space radar telemetry", which General Jacob Carter calls BS on. In truth it's a case of Remember When You Blew Up a Sun?, rewarding the two of them for taking out Apophis' motherships in "The Serpent's Lair". (Daniel and Teal'c aren't eligible, being civilians.)
- Real Life Writes the Plot: It can be reasonably assumed that Sha're's pregnancy was because of her actress Vaitiare Bandera's real-life pregnancy, by her then-boyfriend and on-screen husband Michael Shanks.
- Remember When You Blew Up a Sun?: Jack and Sam are given the Air Medal for stopping the first attempted Alien Invasion against Earth in the series.
- Two Lines, No Waiting: This episode has two entirely disconnected plot threads, one on Abydos and one in Washington.
- Spell My Name with an "S": When O'Neill is unable to convince Selig not to run his story:O'Neill: If you're gonna go ahead with it, I wanna make sure you get one thing right: it's O'Neill, with two 'L's. There's another Colonel O'Neil with only one 'L', and he has No Sense of Humor at all.
- Star-Crossed Lovers: Daniel and Sha're are reunited for all of one episode before being ripped apart again at the end of it.
- Stock Footage: Pretty much every Establishing Shot on Abydos is recycled footage from the Stargate movie. The movie's footage of Ra's ship taking off is played backwards to become footage of Heru'ur's ship landing. Additionally, the episode's other storyline features some stock establishing shots of Washington, D.C..
- Thousand-Yard Stare: O'Neill has a pretty bleak one after Selig dies in his arms.
- Throwing Your Sword Always Works: O'Neill throws his knife at Heru'ur and it conveniently manages to pierce right through the center of the hand device.
- Trojan Prisoner: Teal'c and Daniel attempt to get past Heru'ur this way, with Teal'c disguising himself as a guard and pretending Daniel is his prisoner.
- Tyke Bomb: Sha're states that her baby was intentionally created by Apophis and Amaunet for the purpose of becoming Apophis' next host.
- Wham Shot: Two in quick succession at the beginning of the episode; first when it's revealed that Sha're is inside the tent, and then when she stands and we see that she is heavily pregnant.
- You See, I'm Dying: Jacob tells Sam that he has cancer, which is why he's so keen to see her "fulfill her dream" by joining NASA.