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.

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

SG-1 arrives on a planet where a culturally 'medieval Catholic' community lives in fear of an Unas they believe to be a demon, 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 is faithful to Sokar and fears his authority, which rests on his right to select the 'damned soul' to be sacrificed, has been challenged, so he declares Teal'c a demon and incarcerates all SG-1. Witch-trial-type ordeals see the Jaffa 'proven' a demon and executed by drowning, and Daniel refuses the canon's warning to leave immediately. When Teal'c's symbiote allows a resurrection even Sam hadn't expected, they are all designated possessed and sacrificed, along with Mary. Simon follows the Unas with a staff weapon to liberate them, but he's not alone.

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?

The SGC is contacted by an advanced and embattled alien human civilization seeking military assistance, but their exact reasons for it become increasingly suspect.

An old love of Teal'c approaches the SGC and the Tok'ra claiming that her Goa'uld symbiote has been convinced to defect with their help.

Col. O'Neill and Teal'c realize they and their friends are trapped in a time loop.

The SG-1 team awake to find they have lost their memories. They believe they are workers in an underground power station. They are told that they are helping to preserve life during an ice age. In truth, they are slave labor to a huge domed city above. When Teal'c starts to recover his memory and is given another amnesia treatment, he forgets his Kelno'reem and starts to die. Will the others recover their memories in time to save him?

When Cassandra collapses at home, she is taken to the SGC for treatment. A retrovirus is causing her to emit an EM field and she expresses a need to return to her planet for an initiation ritual. SG-1 investigates and finds a Goa'uld laboratory, probably having belonged to Nirrti, meant for experimentation on the planet's population. They find that the ritual is part of the experiment, a time when Nirrti studies her subjects and cures them when she is done. SG-1 has found a way to cure Cassandra, but now all that remains to be found is Nirrti.

SG-1 teams up with a Russian task force to investigate the disappearance of a Russian SG team on P2X-338. They discover that the Russian SG team released a creature that killed Marduk, a Goa'uld, in his sarcophagus. SG-1 must trust their Russian partners in order to escape the ziggurat alive.

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.

A new leader has risen among the Free Jaffa, K'tano, former First Prime of Imhotep. SG-1, accompanied by Bra'tac, seeks an alliance between the Tau'ri and the large force he has amassed.

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.

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.

After Sam receives an emergency call from geneticist Dr. Richard Flemming, the SGC learns that he has been working for Immunotech, a company owned by Adrian Conrad, who implanted himself with a Goa'uld symbiote in order to cure himself. Fleming has now gone missing and General Hammond orders Sam, Jonas and Teal'c to investigate. They head to Oregon where Fleming lived and worked and learn from the local Sheriff that Fleming isn't the first Immunotech worker to disappear. The locals are acting strangely and seem to suffer from memory lapses. What they eventually find is a town full of Goa'uld and NID seemingly aware of everything that is going on.

Stargate Command is approached by representatives of Jonas Quinn's home planet seeking military hardware. Their world is divided into three territories and there is a long history of war among them. Jonas' country fears that the other two territories are about to sign a non-aggression pact thus making them vulnerable to attack. In return for arms, they are offering an abundance of Naquadria. SGC isn't about to get involved in what amounts to a civil war but there's another possible outcome when Jonas' one-time professor, Doctor Kieran, tells them of an underground movement ready to overthrow the government and seek out a lasting peace. SG-1 travels to Jonas Quinn's home planet to obtain information on the situation there but not all is as it seems.

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.

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

While exploring a crashed alien ship full of passengers in cryostasis, an alien force has downloaded a number of their consciousnesses into Daniel.

Having obtained permission to live off the base, Teal'c rents an apartment, telling neighbors that he has recently arrived from Mozambique. He's under orders to keep a low profile but can't seem to help himself when it comes to helping his neighbors. He helps one who is about to be assaulted by three thugs, but it's his next-door neighbor who seems to need assistance. Krista is having problems with her boyfriend, Doug. Teal'c soon realizes that Doug is beating her and warns him that should he hurt her, Teal'c will kill him. It all becomes very difficult when Doug is found dead in Krista's apartment. Daniel Jackson soon after receives an offer - translate a Goa'uld text, and he will get ironclad evidence that Teal'c is innocent. Meanwhile, Carter is shocked when her boyfriend Pete Shanahan tells he asked for a transfer to the local police department and asks her to marry him.

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.

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.

With the threats of both the Replicators and the Goa'uld greatly diminished and the sister ship to the Prometheus, the Daedalus, now under construction, SG-1 is anxious to get a ride on the new ship. However, the mood is somewhat darkened by a phone call informing Dr. Jackson of Catherine Langford's death. After the funeral, Catherine's niece gives Daniel "a few odds and ends" that her aunt wanted him to have. Upon delivery it is discovered that almost her entire collection was shipped to Daniel's lab. He finds in one of her books a possible location of a ZPM, but scans of the area showed that it was no longer there. Daniel proposes that they use the Ancient's time machine to take it from Ra at Giza in 3000 BC.

SG-1 returns early from a mission only to realize that they and Gen. Landry aren't on the same page as far as the the mission they've just completed is concerned. The confusion is quickly resolved when the "real" SG-1 returns at the correct time. Dr. Lam examines them all and concludes that they are identical and thinks they might be clones. Sam however thinks they may have come from a parallel universe as the result of the black hole they created when they destroyed the Ori beachhead. As more SG-1 teams arrive from other alternate universes, one of them includes Dr. Fraiser and another includes the Tok'ra Martouf. It's left to Sam and Martouf to find a way to send them all home.

While investigating the source of an addictive corn-like crop, SG-1 becomes involved in a firefight. They are forced to fall back to the gate, but as Daniel is dialing both the Stargate and the DHD are beamed away.

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

Vala is kidnapped by agents of the Trust who are trying to find an ancient treasure when an accident causes Vala to forget who she is.