Colonel Jack O'Neill is brought out of retirement to lead a new expedition back to Abydos, only to find an old friend, a new enemy and a far wider use of the Stargate.

With the Stargate program in danger of being terminated, the team is under pressure to find technology. Visiting a planet where they believe there is a creature that possesses the secret of invisibility, they encounter Apophis and his guards. Both sides receiving mortal wounds, they are aided by the planet's inhabitants, the Nox, a gentle people with a very large secret.

SG1 travel to a planet where Teal'c is recognised as once having been head Jaffa to Apophis. He is arrested for the murder of a villager and put on trial for his life. Then other Jaffa attack the village. Will SG1 be able to save Teal'c and prove that he has changed allegiance?

The Stargate team must justify the project's continuation when a doubtful senator, Head of the Congressional Military Appropriations Committee, comes to review the project's performance.

General Hammond has tried everything to get the Senate's decision to shut down his Stargate program undone, but the President personally refuses to 'commit political suicide': the Stargate will be buried. Daniel's insistence -that the danger for Earth as a whole outweighs everything- convinces his colleagues to ignore Hammond's command and dial the address that the Goa'uld invasion started from in the alternate reality that he visited. They arrive not on a planet but a new, superior type of starship, already launched by hyper-drive. A 'video' proves it belongs to Apophis, who gives command to his son Klorel, whose host is none other than the team's young Abydonian friend, Skaara. Overpowering Skaara seems their best move, while Sam installs explosives in the death glider deck with a 24-hour timer just in case, but the Jaffa manage to liberate Klorel. Jack discovers that the ship goes far faster than expected.

As the Goa'uld attack fleet approaches Earth, all four members of the SG-1 team are taken prisoner. They get help from an unexpected source when Bra'tac, Teal'c's mentor, reveals that he is on board. Apophis has delayed the attack until his son Klorel is revived, giving them some time to prepare. SG-1 has used all of the C4 on one of the two ships but must find a way to dispose of the second. Back at Stargate Command, Lt. Col. Bert Samuels arrives as a Pentagon liaison officer but also reveals a new weapon they have developed. General Hammond is dubious. They begin to transport humans to an Alpha site in order to ensure the continuation of mankind.

Teal'c's son Rya'c is kidnapped by Apophis and SG1 tries to rescue him. When Rya'c is recovered he denounces his father and helps to capture the team. They escape, but will they be able to return to Earth and cure Rya'c?

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.

Following on a Tok'ra tip, SG-1 goes to a planet where they find the hated Apophis, nearly dying and under attack by death-gliders. They get back with him, realizing he was tortured by a rival system-lord with lasting harm. Apophis demands sanctuary, provided Dr. Fraiser can save his life, at least on account of the human host, but without a sarcophagus the prognosis for his symbiont is lousy; he offers all his Goa'uld knowledge in exchange for a new host, i.e. his life, revealing he was defeated by the terrible Sokar, once supreme system lord till an alliance lead by Ra and Apophis unseated him. The confrontation with Daniel, on account of Amaunet/Sha're and their son Klorel, and with former prime Teal'c, is bitter for all three. The Tok'ra send Martouf to warn the Tau'ri must hand over Apophis, but their warning is ignored- until Sokar proves he can bombard the iris with accelerated particles and ultimately cut through it, so the White House orders his extradition, but before they can he dies, unlike his host, an Ancient Egyptian temple scribe of Amun.

Colonel O'Neill awakens and is told by new staff everything in the SGC is different because he was just revived after 79 years of cryogenic hibernation, as sole survivor of a disastrous SG-1 mission on a Goa'uld-ruled planet. He accepts to undergo a 'high tech hypnosis' to retrieve information of use in the present war against them, which is going badly, involving earth's ten endangered colonies on other planets. However Major General Trofsky, the new base commander, and his female assistant tell Daniel and Sam, in different sections, that each of them is the sole survivor: it's all make-believe to probe their brains about the weaknesses of earth and the Alliance of the four races. Meanwhile, Teal'c awakes on earth, where it took Dr. Frasier months to save him from death; there was no trace of his teammates, and he resigns when General Hammond refuses permission to keep searching. O'Neill hears Goa'uld language, gets himself free and discovers he's on a fake SGC, frees Sam and Daniel, only to be stopped by the female Goa'uld system-lord Hathor, who employs both Horus and Serpent Jaffa and demands the humans' help against her rival system-lords.

Alternate reality versions of Kawalsky and Carter are caught at Area 51 after coming through the quantum mirror.

SG-1 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 SG-1 convince them that Apophis is dead before the Jaffa fight to the death?

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.

When a "chosen" boy found on planet Abydos is brought to SGC, he sends a telepathic message, causing Daniel Jackson's personality to undergo disturbing changes. Will the rest of SG-1 be able to solve the mystery of the boy's origin before he becomes a power-hungry warmonger?

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.

To help Teal'c's mind clear again, SG-1 asks Bra'tac to help. Bra'tac removes Teal'c's Goa'uld and Teal'c is forced to remember certain memories of his past in order to get back to the real Teal'c in the end. SG-1 is glad to have him back.

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

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.

A man breaks into Jack's house and hold him at gunpoint claiming that Jack ruined his life. Seven years ago he came upon an Ancient artifact at a garage sale that allows him to see all of SG-1's missions.

SG-1 has changed the course of history and made the SGC virtually non-existent. Doctors Carter and Jackson have helped Brigadier General Hammond to find the Antarctic Stargate, but are not being allowed to help any further. They help Jack to power up the time machine, and he gets Hammond to allow them on the mission to Chulak to find Teal'c.

Following on a Tok'ra tip, SG-1 goes to a planet where they find the hated Apophis, nearly dying and under attack by death-gliders. They get back with him, realizing he was tortured by a rival system-lord with lasting harm. Apophis demands sanctuary, provided Dr. Fraiser can save his life, at least on account of the human host, but without a sarcophagus the prognosis for his symbiont is lousy; he offers all his Goa'uld knowledge in exchange for a new host, i.e. his life, revealing he was defeated by the terrible Sokar, once supreme system lord till an alliance lead by Ra and Apophis unseated him. The confrontation with Daniel, on account of Amaunet/Sha're and their son Klorel, and with former prime Teal'c, is bitter for all three. The Tok'ra send Martouf to warn the Tau'ri must hand over Apophis, but their warning is ignored- until Sokar proves he can bombard the iris with accelerated particles and ultimately cut through it, so the White House orders his extradition, but before they can he dies, unlike his host, an Ancient Egyptian temple scribe of Amun.

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.

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