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.

Stargate Command opens a wormhole to a planet with a black hole in orbit.

Daniel falls victim to an invention that swaps his body with that of a dying man.

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.

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.

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 brings back an Ancient device, the purpose of which is unknown. When Jonas touched it the device activated. Upon reaching the SGC Jonas sees a large red insect fly into a wall, but no one else can confirm his sighting. The SGC is put into lockdown, but nothing is found. Jonas suspects that the Ancient device is causing his hallucinations, but to his dismay it is set to be shipped to Area 51. When Teal'c and Jack see the bugs as well, General Hammond decides to let Jonas take a crack at deciphering the Ancient text on the device.

The Russian SG team brings back a man who claims that his people are being experimented on by Nirrti. SG-1 investigate where the experiments are conducted, with the Russian SG team as backup. The inhabitants worship Nirrti as their god and savior from a terrible plague. SG-1 attempts to use the same device Nirrti used on the people to reverse the mutations, but the people turn on them at the arrival of Nirrti.

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

On a shakedown cruise of the Prometheus, the ship's hyperdrive regulator becomes irreparably damaged. A nearby planet was listed on the cartouche of addresses found on Abydos and thus may have a stargate. After a short jump towards the planet, the Naquadria reactor overloads and must be jettisoned. After the reactor explodes above the planet causing damage, the fate of SG-1 and the crew of the Prometheus is in the hands of a once Goa'uld-controlled world that they're off to a rough start with.

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.

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.

When an SG geological exploration mission runs into deadly conflict with an indigenous Unas clan, Daniel gets Chaka to help seek an accord with it.

The president has asked that a documentarian go to SGC to create a film about its operations. His arrival is unwelcome to most and he begins to clash with the base personnel. Nevertheless, he conducts his interviews with SG-1 and the scientists in the employ of SGC. Meanwhile, an off-world SG team finds the remains of an Ancient city.

SG-1 is tasked to accompany members of the International Oversight Advisory, including Richard Woolsey, on a tour of the Gamma site. The visitors are suitably impressed but everyone is put in danger when a carnivorous insect escapes from the lab. The base is locked down and no one is allowed to travel through the gate. The bug is linked to the Ori - it's appeared on several planets that they've visited - and Daniel thinks it may be their follow-up to the virus. SG-1 and the IOA visitors take refuge in a cave, but Gen. Landrey is left with little choice but to flood the planet with a deadly neurotoxin to destroy the bugs. SG-1 looks for away out before that happens.

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.