While 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.

When Teal'c makes Sam Carter realize how valuable the knowledge left by Tok'ra Jolinar in her brain and the chance for an alliance can be, they convince General Hammond to let SG-1 attempt a meeting. They arrive on a planet which is deserted on the surface, but are awaited by well-camouflaged, armed Tok'ra who bring them to tunnels which they create by means of a mysterious crystal, which can also undo them afterward. Both parties are quite suspicious, the team feels like captives, and indeed, the Tok'ra leader Yosuuf fears they cannot be released, at least until the whole site is moved. Meanwhile, the Tau'ri barely overcome their suspicion against the Tok'ra Goa'uld biology (with symbiote), when asked to volunteer themselves as 'hosts', and Carter learns Martouf (and his symbiote, Lantash) was Jolinar's lover, hence has a special connection with her.

The attempt to forge an alliance with the Tok'ra seems a miserable failure, as SG-1 is practically imprisoned as a security risk and considered virtually hostile because 'blending', by agreeing to host a symbiote, is a bridge too far for each of them. When SG-3 arrives and informs Sam about her terminally ill father General Jacob Carter's quickly worsening condition, she realizes the symbiote's healing powers, confirmed to apply to cancer, make hosting an offer to good to refuse for him. Garshaw allows Sam and Jack to return and convince both generals to allow the plan, which is achieved. Meanwhile, the Tok'ra must hastily evacuate, destroying tunnels behind them, because a large-scale attack by Apophis's troops is expected soon, while Jacob meets his potential symbiotic partner Selmak and his equally terminal predecessor to help him decide. Jack verifies his strong suspicion there is traitor among the Tok'ra who is communicating with the Goa'uld.

When an incoming wormhole is established at the SGC, the iris is over-ridden and opened. A young boy appears and tells the SGC that they are in terrible danger from a group of terrorists. But these terrorists are invisible creatures and they are determined to wipe out all humans to prevent them being used as hosts to the Goa'uld.

Sam's father hopes that SG-1 can help find and neutralize Seth, an Ancient Goa'uld who the Tok'Ra believe may still be hiding on Earth after thousands of years.

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, where prisoners are sent to suffer eternal torture, and from where no one returns; only Jolinar has 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 the custody of Netu's lord Bynarr, does Sam realize he is the key, in a 'personal' way, but not voluntarily, as she had thought. Sokar learns of their presence from Bynarr and orders the 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 that 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.' Apophis also implants a memory device in, and gives the drug to, Jack to torture him using the persona of his young son that died, and Daniel for the location of his Harsesis son. Martouf's love for Jolinar makes him betray that the Tok'ra are on planet Entac - 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 when his ship arrives as their last chance to eliminate Sokar, but he decides to rescue SG-1 instead, by flying in the path of the rings device on Sokar's ship when he arrives.

While testing a new spacefighter made from Goa'uld parts, Col. O'Neill and Teal'c are trapped when a hidden automatic recall function takes over and sends it into space.

Teal'c is on his home planet, Chulak, where there is rebellion among the Jaffa warriors. He is betrayed as a sacrilegious shol'va (traitor) by Rak'nor, son of a Jaffa friend of his father, and handed to Terok, the torturer of system lord Heru'ur. Ignorant of his fate, the other SG-1 members join Jacob in a risky attempt to take hold of a space mine using a Tok'ra ship piloted by Jacob. En route to Apophis' spaceship, the expedition finds out that Teal'c is being offered as a confidence-building present from Heru'ur to cement an alliance with Apophis against the other system lords, which would make the Goa'uld threat more dangerous than ever. They decide to save Teal'c, but their attempt fails. However, Teal'c's resistance to torture and clear conviction that Goa'uld are not gods finally convinces Rak'nor, who now bravely acts.

SG-1 delivers their newly confiscated Goa'uld mothership to help the Tok'ra evacuate their planet and deal with their disinformed Goa'uld spy in their midst.

Stranded in another galaxy while fleeing their attack on Apophis' fleet proves only the beginning of SG-1's problems as multiple enemies appear.

In a Tok'ra plan to wipe out the Goa'uld, Daniel goes undercover as Yu's servant to release a poison at a meeting of the system lords. Meanwhile a Goa'uld attack on the Tok'ra base leaves the rest of SG-1 with their hands full.

As the Goa'uld summit continues, Daniel finds himself face to face with Osiris. He fools him in the same fashion as he did with Yu, but cannot bring himself to cause the death of Sarah, Osiris's host. He remains to uncover information about the unknown master of Osiris. Lantash, having taken Lt. Elliot as a host, guides the rest of SG-1 in escaping the fallen Tok'ra base.

As Jackson suffers from a fatal dose of radiation, he struggles with the value of his life while his friends deal with the emotional and diplomatic repercussions.

When SGC detects an Goa'uld ship in orbit, SG-1 is dispatched with Jacob Carter to investigate. They find the ship to be abandoned with no discernible life signs and Sam determines it to be the same used to kidnap Thor. Once on board the Goa'uld vessel, they find that the crew had initiated a self destruct sequence. O'Neill would very much like to salvage the ship despite Jacob's warnings that it could be a Trojan horse. An examination of the computer core reveals that Thor may have been able to introduce a virus but Jacob was right: it's an ambush and the ship soon plunges in the ocean. SGC and the Navy mount a rescue operation.

The Tok'ra are forced to evacuate their newly established base under attack from the Goa'uld. They flee to the SGC's Alpha site. Tensions rise between the allied factions, the Free Jaffa, Tau'ri, and Tok'ra. Jacob and Selmak feel the end of the Tok'ra is near and Sam finds a Naquadah generator has been sabotaged to function as a bomb. Jack suspects the recently arrived Tok'ra and attempts to weed out the traitor.

The US and Russia reveal Stargate Command and its operations to representatives of the other permanent members of the United Nations Security Council.

Teal'c is having strange nightmares featuring Apophis in which he is human and a firefighter with the rest of his team alongside him.

A teenage boy shows up at the SGC claiming to be Jack O'Neill. He recalls a dream in which an Asgard was studying him. They determine that they must find this Asgard to fix what has been done to Jack.

Bra'tac and Teal'c encounter a heavily armed enemy with shielding protecting him from Goa'uld weaponry who took out two Goa'uld personal guards. They barely manage to defeat him and bring him back to SGC for study, but this new threat poses a greater problem for the Tau'ri.

The Tau'ri and Tok'ra have used their captured super-soldier to determine his planet of origin. With Daniel, Dr. Lee, and the Ancient device they found in the hands of Honduran kidnappers, SGC must find a way to retrieve them if they are to have any chance of defeating the newly encountered super-soldiers.

During an engine cool down break from hyperspace travel the crew of the Prometheus, with Major Carter as an advisor, encounter a space craft of unknown configuration. They hail the ship to no avail; the unknown craft opens fire upon the Prometheus. Carter attempts to override the safety protocols on the hyperdrive to make a short jump into a gas cloud, but in the attempt is knocked unconscious. She awakes to find the ship devoid of all its crew and, as she tries to escape the gas cloud by herself, she begins to hallucinate.

At the new Alpha site, Sam Carter and Selmak (the symbiote carried by Jacob Carter, her father) are working on a new weapon to defeat the Anubis superdrones when the planet is attacked by a fleet of Goa'uld ships. Carter escapes with the prototype weapon before the base auto-destruct is activated but finds herself being pursued by a superdrone.

The newly inaugurated President of the United States is briefed by the Head of the Joint Chiefs of Staff on the Stargate program. Former Senator, now Vice President, Kinsey attempts to get his running mate to back his policies for the program, but the president decides to look into the situation himself. Kinsey gets Richard Woolsey to convince the president of his agenda.

After a long absence, Jacob Carter returns to the SGC to tell Jack that the galaxy is under threat of takeover by the Replicators. The Goa'uld are under attack from the Replicators and are quickly being eliminated. Ba'al's armies are being destroyed and he arrives at SGC to suggest they work together to defeat their common enemy. Carter's doppelganger, RepliCarter, is leading the attack and she has kidnapped Daniel Jackson in the hope of learning of any weapons the Ancients may have created that could defeat them. Jackson gets help from an unexpected source - the Ancient, Oma Desala - or so he thinks.

Sam and Jacob are on the planet Dakara trying to configure the Ancient's device to destroy the Replicators once and for all, helped partly by Ba'al and Daniel, who succeeds in freezing the Replicators by manipulating Carter's duplicate.

Daniel finds himself in a strange time and place - a diner where Oma is working as a waitress. She gives him a clear choice - he can choose to die or to ascend but if it's the latter, he will not be able to help his friends fight Anubis, who has yet to be disposed of. He strikes up a conversation with another patron, Jim, who has his own take on the situation. Meanwhile, Sam decides the time has come for her fiancé to meet her father, Jacob. Jacob is not well, however, something he has kept from Sam for several weeks. After Pete surprises her - he thinks he's found the perfect house for them - Sam realizes she has to come to grips with her feelings for someone else. Teal'c and Master Bra'tac have information that Anubis may be gathering what remains of his forces for an attack on Dakara.

The attempt to forge an alliance with the Tok'ra seems a miserable failure, as SG-1 is practically imprisoned as a security risk and considered virtually hostile because 'blending', by agreeing to host a symbiote, is a bridge too far for each of them. When SG-3 arrives and informs Sam about her terminally ill father General Jacob Carter's quickly worsening condition, she realizes the symbiote's healing powers, confirmed to apply to cancer, make hosting an offer to good to refuse for him. Garshaw allows Sam and Jack to return and convince both generals to allow the plan, which is achieved. Meanwhile, the Tok'ra must hastily evacuate, destroying tunnels behind them, because a large-scale attack by Apophis's troops is expected soon, while Jacob meets his potential symbiotic partner Selmak and his equally terminal predecessor to help him decide. Jack verifies his strong suspicion there is traitor among the Tok'ra who is communicating with the Goa'uld.

Stranded in another galaxy while fleeing their attack on Apophis' fleet proves only the beginning of SG-1's problems as multiple enemies appear.

Daniel finds himself in a strange time and place - a diner where Oma is working as a waitress. She gives him a clear choice - he can choose to die or to ascend but if it's the latter, he will not be able to help his friends fight Anubis, who has yet to be disposed of. He strikes up a conversation with another patron, Jim, who has his own take on the situation. Meanwhile, Sam decides the time has come for her fiancé to meet her father, Jacob. Jacob is not well, however, something he has kept from Sam for several weeks. After Pete surprises her - he thinks he's found the perfect house for them - Sam realizes she has to come to grips with her feelings for someone else. Teal'c and Master Bra'tac have information that Anubis may be gathering what remains of his forces for an attack on Dakara.

When an incoming wormhole is established at the SGC, the iris is over-ridden and opened. A young boy appears and tells the SGC that they are in terrible danger from a group of terrorists. But these terrorists are invisible creatures and they are determined to wipe out all humans to prevent them being used as hosts to the Goa'uld.

Sam's father hopes that SG-1 can help find and neutralize Seth, an Ancient Goa'uld who the Tok'Ra believe may still be hiding on Earth after thousands of years.

At the new Alpha site, Sam Carter and Selmak (the symbiote carried by Jacob Carter, her father) are working on a new weapon to defeat the Anubis superdrones when the planet is attacked by a fleet of Goa'uld ships. Carter escapes with the prototype weapon before the base auto-destruct is activated but finds herself being pursued by a superdrone.

While testing a new spacefighter made from Goa'uld parts, Col. O'Neill and Teal'c are trapped when a hidden automatic recall function takes over and sends it into space.

SG-1 delivers their newly confiscated Goa'uld mothership to help the Tok'ra evacuate their planet and deal with their disinformed Goa'uld spy in their midst.

Teal'c is on his home planet, Chulak, where there is rebellion among the Jaffa warriors. He is betrayed as a sacrilegious shol'va (traitor) by Rak'nor, son of a Jaffa friend of his father, and handed to Terok, the torturer of system lord Heru'ur. Ignorant of his fate, the other SG-1 members join Jacob in a risky attempt to take hold of a space mine using a Tok'ra ship piloted by Jacob. En route to Apophis' spaceship, the expedition finds out that Teal'c is being offered as a confidence-building present from Heru'ur to cement an alliance with Apophis against the other system lords, which would make the Goa'uld threat more dangerous than ever. They decide to save Teal'c, but their attempt fails. However, Teal'c's resistance to torture and clear conviction that Goa'uld are not gods finally convinces Rak'nor, who now bravely acts.

Bra'tac and Teal'c encounter a heavily armed enemy with shielding protecting him from Goa'uld weaponry who took out two Goa'uld personal guards. They barely manage to defeat him and bring him back to SGC for study, but this new threat poses a greater problem for the Tau'ri.