Aptly titled, there are a whole bunch of secrets in this episode. Sam keeping the secret of the work she's doing from her father, the secret harcesis child of Apophis and Amonet's host, Sha're, then Kasuf hiding the child from the goa'uld, Amonet not revealing SG-1 to Apophis and his guards, and last but not least, the reporter who has discovered the secret of the Stargate program.
Two concurrent stories are shown; Sam and Jack going to Washington, D.C. to receive medals from the President, and Daniel returning to Abydos as he promised them a year ago, along with Teal'c. Sam's father, Jacob, is also present at the medal ceremony, and is trying to meddle with her career and get her into NASA, so she can follow her dream and go to space. Sam, obviously, doesn't want to go in a tiny shuttle all the way out to orbit when she routinely goes lightyears away to other planets around the galaxy. Meanwhile a reporter approaches Jack looking for details about the Stargate program, about which he already knows a lot, meaning there's a leak somewhere. On Abydos, Daniel and Teal'c find Daniel's wife Sha're, who is not under the influence of the goa'uld Amonet due to being heavily pregnant, and the goa'uld not wishing to risk the life of the child, whom Apophis wishes to be his future host.
Sam does a pretty awful job of keeping her cover story intact to her dad, who knows it's a cover story, but doesn't pry too much. He's baffled by Sam's insistence not to take the opportunity he's created for her to join NASA, though, and of course she can't tell him the real reason. Conversely, Jack keeps an air of aloofness (not hard for him, I know...) when confronted by the reporter, and even manages to think up a quick explanation for being caught talking about navigating the galaxy. Unfortunately, the reporter is run down by a car before he can report on his findings, which leaves Jack very suspicious.
It's never made clear if this is actually an accident or whether the DoD arranged his death to avoid the story breaking. Regardless, Jack thinks it was no accident, and when told by general Hammond that "it wasn't us", his eyes betray his feelings. It's brilliant acting by Richard Dean Anderson, and shows disappointment in his superiors and 'the system', and sadness that it had to come to this. Carter says her goodbyes to her dad, who tells her quite bluntly that he has terminal cancer.
Afterwards, Jack and Carter head to Abydos to find Heru'ur there, who came to steal the baby, but he escapes (baby-less) and not a second later, Apophis turns up to take Amonet. She tells him that Heru'ur has the baby, which is what Teal'c tried to lead her to believe, but she looks right at SG-1 before leaving, so she knows that's not the case. She keeps her mouth shut, though. Is she, too concerned about the baby's fate? Is she plotting against Apophis (Knowing the goa'uld mindset, this isn't hard to believe)? Or is Sha're exerting some control over her, the way Skaara managed to overpower Klorel for a few seconds in The Serpent's Lair?
This question goes unanswered, as does my own wondering why Daniel didn't carry Sha're off to Cimmeria to go through the new Thor's Hammer device? Maybe he feared for the child's safety through the ordeal, and wanted to take her after the birth, but ran out of time.
The episode did a good job of moving the main story forwards, and features some of the best acting from Richard Dean Anderson, which is the highlight for me. It also introduces Jacob Carter, who'll become an important, and likeable, recurring character.