Ready to go on vacation, O'Neill is beamed away by the Asgard. Thor tells him that Earth is faced with an enemy even worse than the Goa'uld.

SG-1 has to deal with a Replicator infestation on a Russian sub on Earth while Major Carter advises the Asgard about combating the menace in their galaxy.

The SGC is visited by a Tok'ra named Anise who brings some armbands used by the soldiers of a long extinct race, which are supposed to increase the abilities of the wearers. O'Neill, Carter and Jackson put the armbands on and it increases their physical strength, but it also causes them to make rash decisions. Can they get the armbands off before they cause their deaths?

When an SG-team member tries to assassinate the Tok'ra leader, it is believed that some of the SGC have been converted into Za'tarc - programmed assassins. The Tok'ra Freya comes to the SGC with Martouf to try and test all SG-team members. But the Za'tarc detector suggests that O'Neill and Carter are actually Za'tarcs. Is this correct and is there another Za'tarc at the SGC?

The SGC learn that the Russians have a Stargate of their own and they need the Americans' help with their problems with it that are affecting them both.

On the Enkarans' new home, SG-1 discovers a giant spaceship is threatening the colonists as it terraforms the planet.

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.

General Hammond mysteriously retires from the SGC and a new general is brought in, who breaks up SG-1: Daniel and Sam are scientists, Teal'c is with SG-3 and O'Neill commands a new SG-1. O'Neill tries to convince Gen. Hammond to return, but he finds out that someone ordered Hammond to leave or they would hurt his grandchildren. While the others are occupying the new general, O'Neill tries to find out who that "someone" is. Thereto he must place his trust in the one person he hates most: Maybourne.

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

When SG-1 inadvertently dooms a planet upon arrival, the team must overcome Asgardian diplomacy and indigenous religious prejudice to put things right.

A strange ship is headed towards Earth, and the SGC suspects that Martin Lloyd and his companions may have something to do with it. O'Neill is sent to speak to Martin and is assigned as a military consultant on Martin's new show, "Wormhole X-Treme!", which uncannily resembles SG-1 despite Martin once again losing his memory. His former shipmates stall Carter and Daniel by throwing them off the trail and into the hands of the NID.

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.

While still dealing with the loss of Daniel Jackson the SGC is contacted by the Asgard who require assistance dealing with Anubis, who seems to have new shield technology that can repel Asgard weapons.

Master Bra'tac arrives with bad news: Teal'c's wife is deathly ill, and Teal'c leaves to be with her. Shortly thereafter, the gate is opened but nothing comes through. Then Carter discovers a very low power signal that is slowly building an overload powerful enough to destroy the Earth.

Anubis' weapon continues to threaten Earth. Various plans are tried until Jonas Quinn suggests something simple that just might work. Meanwhile, Master Bra'tac has discovered the planet from which Anubis is launching the attack. He, Teal'c and Rya'c journey there to put a stop to it.

SG-1 is providing security for three scientists who are conducting research on a far-off planet. Goa'uld warlord Khonsu arranges to capture the SG-1 team and O'Neill tells Jay Felger, nominally the group's leader, to use the gate and head back to SGC. Felger is quite enamored with SG-1, admiring their exploits and daring-do. Rather than follow O'Neill's orders, Felger and another scientist, Simon Coombs, transport themselves up to the Goa'uld ship. What the scientists don't know is that SG-1's capture is a ruse to allow Khonsu, who is actually a Tok'ra, to pass on information. O'Neill is quite annoyed with the two scientists but their presence proves useful in the end.

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

Riding in the elevator in the SGC, O'Neill is visited by Daniel Jackson who needs his help. Daniel tells him that Anubis is headed for Abydos to search for something called the Eye of Ra, a relic that would make Anubis all-powerful. It's essential that SG-1 go to Abydos and secure the Eye but no has seen it - including Daniel - nor has anyone ever been able to find it. On the planet they see their old friend Skaara and with Daniel's help locate the Eye. They also find a tablet that speaks of a lost city of the ancients. When Anubis and his troops land in force there is little anyone can do to stop them. In the end it's left to Daniel to decide if he will try to stop Anubis - thereby breaking a cardinal rule of the Ancients.

A group of nomads on an alien planet find Daniel Jackson naked in the middle of ruins and take him in. Jonas translates the tablet Daniel said was important and discovers that it describes the last city the Ancients were building before the plague. He surmises that the list of addresses Jack put into the computer while storing the Ancient data were Ancient outposts in temporal order. Thus the last of the addresses should be the "City of the Lost". SG-1 visits the planet and happens upon the nomadic people, now inhabiting the ruins of the Ancient city. There they find Daniel, but discover his memory is gone. They must recover his memories in order to discover the secret to defeating Anubis.

In a firefight with Jaffa, Teal'c takes a staff blast to the gut. Without his symbiote, he cannot regenerate as he once did. Daniel feels that he cannot remember something important, so he goes searching through the logs for any sign of his lost knowledge. Teal'c expresses his feelings that the Tritonin has made him weak.

SG-1 investigate a seemingly idyllic and subtly advanced human colony sheltered inside an energy dome on an otherwise inhospitable planet.

To save his job, Dr. Felger tests a new virus on the Stargate Network to help control it and it ends up disabling it instead.

Jonas Quinn returns to the SGC to ask for assistance in saving his nation. He explains that the Naquadria was originally Naquadah and a Goa'uld named Thanos started a chain reaction to transform all of his planet's Naquadah into Naquadria. A large vein of Naquadah has just been affected and the Kelownan scientists believe that the transformation will cause this large a deposit to explode, taking their entire nation with it.

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.

Vice President Kinsey briefs Dr. Weir on the Stargate program before her meeting with the president. SG teams 1, 3, and 5 go off-world to attempt the extraction of a newly found Ancient repository device. Upon arriving at the location of the device, SG-1 comes under fire from Goa'uld ships. With no other way to disallow Anubis from claiming the knowledge for himself, Jack submits himself to the dangerous device.

The Asgard fleet has managed to destroy the Replicator ship, with Carter aboard, but cannot contain the debris. Talks break down with the System Lords, ending in a Ha'tak being dispatched to test Earth's new defensive capabilities. The Prometheus waits to engage the incoming enemy, but Thor arrives in the Daniel Jackson, with Teal'c aboard. They enlist the help of Daniel and Jack, still in stasis, to remove the threat of the replicators to the new Asgard homeworld.

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.

Martin Lloyd seeks out SG-1 for assistance when his failed TV show based on the real Stargate program becomes a feature film.