O'Neill, Carter and Jackson are trapped on Hathor's planet. Teal'c and Hammond go to Chulak to forge a rescue plan and recover the team.

Stargate is visited by general Jacob Carter on a mission -actually requested by his symbiont Selmak, who wants him to deal with his long-repressed break-up with Sam's brother Mark- to ask SG-1's help in the hunt for the sole system-lord the Tok'Ra never tracked down, Seth, the Egyptian god of chaos and total evil, who plausibly never left earth but hides as Ra put a high price on his head. Daniel finds a plausible series of Seth-cults, each ending in a blood-bad for followers, the latest being outside Seattle, led by Seth Fargo. Jacob and SG-1 arrange to take over the case jurisdiction from the ATF by presidential intervention. As Daniel predicts, they find escape tunnels and get in, but are awaited and disarmed, to be exposed to nish'ta, a powerful biological submission drug, and when Seth senses Jolinar's traces destined for elimination...

The Asgard and three Goa'uld System Lords meet at Stargate Command to negotiate a treaty modification, but subterfuge and treachery threaten not only the success of the negotiations, but Earth itself.

SG-1 discover nine Goa'uld corpses in a sealed chamber, Teal'c identifies the crest as the nine Linvris, minor rivals of the system lords. While reading a tablet containing page one of some war plan, Daniel unknowingly gets infected by a parasite, which gives him visual and auditive delusions back on earth. An epidemic of migraine causes the general to keep all SG-teams in the base for examination. Daniel was already in a padded psych ward cell when during a visit from the colleagues he hears Ma'chello's voice say the parasite has left to enter its real target, a Goa'uld: Teal'c, for whose symbiont it is lethal. During examination of the page turner which released the designer organism, Jack, Dr. Fraiser and Sam get infected by several parasites, only Sam is found immune, even able to kill it by hosting it. The race is on to find how and hopefully use that mechanism to save the other three infected ones...

The planet Orban, with Precolumbian Teotihuacan-culture antecedents and Aztec type pyramids, has made impressive scientific progress, and brings Sam a naquadah reactor to study; when she demands an instructor, Orban official Kalan surprises SG-1 by saying that he does not know what an instructor is, but 11 year-old Merrin stays on base to teach Carter. On Orban, Kalan's son Tomin, another 'urrone' (apprentice) is assigned to exchange knowledge about the Goa'uld with Teal'c and Daniel. SG-1 and Dr. Fraiser are astonished to discover the Orban urrones know neither fun nor school: a mass of useful new information is acquired while they are young and stored in the easily reproducible form of nanites, which are implanted in every Orbanian's brain after the urrone's 'averium', a coming of age ceremony at age 12, which extracts the knowledge from the individual and ends their ability to function mentally, so those children are 'retired' for life and from the active society. The Orbanians are furiously insulted by any suggestion to avoid an averium for the child's sake, yet Jack retains Merrin to let her experience how earth children spend their youth in schooling and play, offering it to her as an alternative to the averium, with a remarkable result...

The quantum mirror Daniel found in "There But for the Grace of God" brings to Area 51 an alternate Kawalsky and Dr. Carter from another reality, this time one where Sam never joined the military but became Jack's wife and the Goa'uld just overran earth. Dr. Carter begins suffering from temporal entropic cascade failure, a paradoxical effect of having two versions of the same person in the same reality and realises that she must return to her own reality or both Sams will eventually perish. SG-1 embark to the alternate reality to intercede and prevent the Goa'uld from conquering Earth before our General Hammond has the mirror disabled. The alternative Teal'c remained Apophis's loyal first prime, so the 'real' one can assume his identity to infiltrate the invading force but they are discovered and captured, but this only serves as the ideal diversion while the Sams also contact the alternate Asgard...

While on a mission to recover a UAV, SG1 are captured by a Bounty Hunter working for evil System Lord Sokar. He tells them there is a bounty on their capture, but offers to let them go if they help him capture a Goa'uld. The Goa'uld turns out to be a Tok'Ra. Can the team persuade the Bounty Hunter to release the Tok'Ra, but prevent SG1 from being handed over to Sokar?

SG-1 lands on a planet where a culturally 'medieval Catholic' community lives in fear of a demon of Unas's species, which regularly collects human sacrifices to Satan, in fact hosts for system lord Sokar's army. When Simon implores SG-1 to spare his beloved Mary and take him instead, they even nurse her chicken pox. Simon hopes they are sent by God to deliver them from the satanic burden, but the canon who rules the village as 'spiritual' leader faithful to Sokar fears his authority challenged, which rests on his right to select the 'damned soul' to be sacrificed, declares Teal'c a demon and incarcerates all SG-1. Witch-trial-type ordeals see the Jaffa 'proven' a demon and executed by drowning, Daniel refuses the canon's to leave immediately. When Teal'c's symbiont allows a resurrection even Sam hadn't expected, they are all designated possessed and sacrificed, yet Mary is also. Simon follows the Unas with a staff weapon to liberate them, but he's not alone...

SG1 come across another SG team being attacked by Jaffa. They offer to help but are shot by the SG team members. When they awake, they find out that the other SG team are Jaffa, loyal to Apophis, who are planning to infiltrate Earth. Can SG1 convince them that Apophis is dead before the Jaffa fight to the death?

Responding to a help cry from Kasuf, SG-1 and more USAF wipe out a Goa'uld Jaffa guard to save most Abydonian slaves. When Amaunet turns her hand device on Daniel, he can't bring himself to shoot his beloved wife Sha're, but Tel'c saves him by fatally staff-shooting her; Abydononian funeral tradition squashes his hope of a sarcophagus resurrection. Crushed by grief, Daniel has apparitions by Sha're and once released from hospital resigns from SGC, claiming the quest for his wife was his reason to join; his former research assistant Dr. Robert Rothman succeeds him in SG-1; Jack is sure he'll be back. Sha're (or Ammaunet's posthumous manual spell?) keeps appearing to Daniel life-like, telling him to forgive Teal'c and together find their boy, who as Harsisis has all the Goa'uld knowledge in his genetic memory, punishable by death. Daniel agrees to return, but has his secret agenda too...

On the planet Vyus, SG-1 discover an entire early industrial society suffering from collective amnesia since an unspecified event about a year ago known as the Vorlix. The most lucid local, scientist Ke'ra, develops an almost amorous relationship with Daniel while she shows the team the fascinating diary of a deceased scientist, which also mention a pesticide Dargol which had to be banned because it affected fertility and a 'visitor' named- Linea, who fits the description of the Destroyer of world SG-1 inadvertently helped escape (in "Prisoners") with them from a penal planet. Ke'ra and a Vyus couple, Orner and Layale, come to star-base where Dr. Frazer proves Ke'ra has Linea's DNA, and the amnesia is caused by a physical block in the brains caused by Dargol, which Linea developed into an experimental fountain of youth, which apparently suddenly went wrong. Manufacturing a medicine within a reasonable time, before ignorance ruins the planet, is hopeless without Ke'ra/Linea, but shouldn't she rather be incarcerated then given the chance to play another diabolical trick if she remembers her evil persona?

Martouf leads a Tok'ra delegation with crushing news for Carter: her father Jacob/Selmak has been captured by Sokar and imprisoned on Netu, an Egyptian name for hell, on a moon of planet Delmal, from where nobody returns to suffer eternal torture, only Jolinar ever escaped. SG-1 mounts a rescue operation with Martouf, top-priority being any information Selmak can offer about Sokar's plan to subjugate the other system lords, an unprecedented threat for all humanoids in the galaxy. Teal'c must pilot a goa'uld ship and keep it in orbit as landing is impossible except by small pod, but first Martouf taps into Jolinar's memory, which is partially blocked by some trauma beyond physical torture. Only when they're down and in custody of Netu's lord Bynarr, Sam realizes he is the key, in a 'personal' way, but not voluntary as she thought. Sokar learns their presence from Bynnar and orders team and craft destroyed, but this also means there must be a way out. Bynarr's prime Na'onak has and is himself a major surprise...

Now Apophis has revealed himself, he promises the prisoners to overturn Sokar, which requires extracting an irresistibly valuable secret, to which end he drugs Sam with the truth serum 'blood of Sokar' and implants a memory device plus the drug to torture Jack in the persona of his dead kid son and Daniel for the location of his Harsesis son; Martouf's love for Jolinar makes him betray the Tok'ra are on planet Etnac- a convincing lie, so Apophis's plan to earn Sokar's gratitude and then kill him when rewarded with the lordship of Netu is on a shaky basis... Teal'c must help the Tok'ra Aldwin prepare a nuclear weapon to explode the whole moon, as last chance to eliminate Sokar when his ship arrives, but decides to rescue SG-1 instead by flying in the path of the rings device to Sokar's ship...

After a vain search for Amaumet and the Harsesis boy on an unexplored planet, SG-1 is told there is a chemical leak and gets sedating injections in the infirmary. In fact star-base has been taken over by body-snatching aliens, as Teal'c and Sam discover, who are immune because of his symbiont and her Jolinar-remnants. Teal'c is captured while giving Sam the chance to escape; she meets with Colonel Harry Maybourne, who alas believes and brought the alien-possessed Jack and Daniel, who claim it's paranoia caused by the leaked chemical; during a flight back, Sam is able to see trough the game because of a 'flicker' and discovers it's done by two electronic devices to assume a human shape and voice. Meanwhile the real Jack and Major Paul Davis awake in an organic web where every human is tied into tentacles, soon meeting up with Sam and liberating Teal'c, in a hurry to try Sam's sound-idea before Maybourne sends in troops with orders to shoot and kill...

The iris brings surprise visitors to Starbase: the cat Schrödinger as sign of friendliness, next Narim, the Tollan admirer Sam gave him to, who brings a unique invitation from the curia, the highest Tollan authority: an invitation to attend on Tollana, their new home planet, the 'Triad', a judicial ceremony, learning only there as requested by seeker (trial party) Skaara, to act a his his 'Archon' (attorney), a job jointly assigned to Daniel and Jack, his claim being his desire to be separated from the Goa'uld Klorel, Apophis's son, who refuses to give up his host; they crashed on Tollana after the Tollans destroyed both mother-ships Heru'ur sent after Klorel. Klorel's archon is the Goa'uld lord Zipacna, reason enough for Jack to be frantically mistrusting of the Tollan assurance all visitor weapons are automatically disabled. The third, neutral archon is Lya, a Nox; the Tollan Travell presides. While the human doctrine of birthright opposes Zipacna's claim of Ra's jurisdiction on Abydos and species superiority, like humans practice on lower animals, Teal'c and Sam fear his Serpent guards are locating the Tollan defensive ion guns to disable them, a nightmare scenario arrogantly laughed away by Travell, so Teal'c asks Ly'as for help. After Zipacna invoked that ruling against Klorel would be an effective death sentence, forbidden under Tollan law, Skaara's side that being a host is no valid life, a Goa'uld mother-ship is reported approaching; the Nox decides the sentence...

The SG1 team embark on a trip to visit a planet with an idyllic beach, but as soon as they step through the stargate, they find they are back in the SGC. They thought that they just left, but have been missing for hours. They soon discover that an alien device has been implanted in their brains and a being called Urgo reveals himself to the team. But no one else can see him and he is extremely irritating. Will they be able to extract him before they lose their minds?

Whilst on a planet to negotiate a trade treaty, SG1 are shown a meteor shower called the 'Fire Rain' by the locals. They are very concerned, when one of the larger meteors enters the atmosphere in a near miss. Carter checks the astronomical data and Jackson the archaeological finds and they discover that the meteors may hit the ground with incredible force. They try to evacuate the villagers, but in the process, the meteors start striking the ground and whilst O'Neill is away trying to find some stray villagers, the Stargate is hit by a large meteor. The SGC try to dial back to the planet, but find that the gate is buried and is lying flat. Can Carter come up with a way to get back to the planet, or will O'Neill be trapped there forever?

While negotiating on the new Tollan home world, SG1 are refused any technical weapons help, so O'Neill steals a defense device. He returns to the SGC and is suspended by Hammond. While on suspension, he is visited by Maybourne and told that there is a team off-world that illegally captures technology for Earth. He offers O'Neill command of this team. O'Neill uses the pretense of retiring off-world to leave through the Stargate. But once off-world, he meets Maybourne's team. Is everything as it appears though?

Whilst redialing old Stagate addresses, the SGC discovers that a gate that was previously buried has become uncovered. They send a probe through and find two archaeologists. However, when they travel through the Stargate, they find that it is located in a in civil war: one continent believes that the people were created by a Goa'uld, whilst their enemy believes that humans arrived from another planet - by the Stargate. O'Neill, Carter and Jackson are captured by the authorities and questioned, but Teal'c is wounded and blinded. Can he help SG-1 escape the hostiles and get back through the Stargate?

Master Bra'tac arrives at the SGC saying Apophis has attacked Chulak. Apparently the Goa'uld search for the Harsesis son of Sharee/Amaunet. Bra'tac believes that the child is in Keb, on a planet the Goa'uld fear too much visit; SG-1 and Bra'tac look there for the boy.

The SGC send a MALP to a huge pyramid and inside they discover a crystal skull like the one Jackson's grandfather found many years before. SG1 visit the planet and whilst Daniel is looking into the eyes of the skull, as his grandfather did, an energy field envelops him. Teal'c fires his Zat at the skull, but Daniel has disappeared. Carter collapses and the team minus Daniel return to the SGC. Teal'c returns to collect the crystal skull, but will he be able to find Daniel?

While taunting Carter leave means leaving to have fun, not staying behind for more research, Jack is suddenly beamed aboard the spaceship of the Asgar Thor, who explains he is dying, and his ship falling victim in the war against the Beliskner to replicators, an all-infesting kind of mechanical bugs which literally devour it to multiply, the transport and self-destruction mechanisms are now also disabled but their next target will be earth if they manage to land. Jack contacts SGC, asking advice and forbidding SG-1 to join him, but they do after the general overrules the colonel, assuring him they have a way back. After Sam makes sense of Thor's notes about the 'techno-bugs' and discusses them with him, she comes up with a plan to explode the ship and the bugs and escape by stargate, but it depends on meticulous timing and Teal'c placing explosives at the outside, which proves even more dangerous then it sounds...