The Stargate Program (SGC) is revived when Apophis, an alien of the same race as Ra, comes to Earth through the gate seeking hosts. After the attack, Colonel Jack O'Neill and Samantha Carter are sent to Abydos to locate, and bring back, Daniel Jackson. O'Neill and Daniel befriend Apophis's first prime Teal'c, a Jaffa (one who is an incubator to a larval Goa'uld), and Teal'c joins their side. He helps SG-1 return to Earth, though they cannot save Daniel's wife Sha're and his friend Skaara, who have been taken as hosts.

After being infested by a Goa'uld parasite in the previous episode, Major Charles Kawalsky shows signs of possession. The symbiote is removed, but Kawalsky remains possessed and is killed by Teal'c.

SG-1 visits a planet inhabited by the Shavadai, a nomadic tribe descended from the Mongols. They regard women as property, and restrict their rights in the belief that to do otherwise would bring "demons" (the Goa'uld) down upon them. Carter ends up being 'sold', but when Carter beats a chieftain in hand-to-hand combat, the team changes the tribe's opinions about the rights of women. 

SG-1 travels to P3X-797, a planet divided into 'Light' and 'Dark' sides. While the inhabitants of the light side have a Bronze Age culture bearing similarities to the Minoan civilization, the dark side is infected with a plague that turns people into savages, and the SGC is locked down when SG-1 brings it home. Dr. Janet Fraiser manages to find a cure for both peoples.

As SG-9 is on P3X-513 and long overdue, SG-1 is sent after them to find out what has happened to them. They soon discover that the commander of SG-9 has gone completely insane and set himself up as a god on the planet.

A strange crystal strikes down O'Neill, replacing him with a double that returns with the team to Earth to find the cause of O'Neill's private grief – his son's death. But the double is dangerously unstable. Can O'Neill return home to save everyone and prevent chaos?

When a planned ambush goes disastrously awry, resulting in fatalities among the SG-1 team, the peace-loving Nox restore them to life. But while these gentle people can bring back the dead, can they resist the deadly technology of the blood-thirsty Goa'uld?

On the mysterious planet Argos, the beautiful Kynthia (Bobbie Phillips) seduces Colonel O'Neill, which means he is condemned to an Argosian lifespan of only a hundred days. As he turns grey and old, will his team succeed in their frantic search for a cure?

SG-1 visits the planet Cimmeria (P3X-974), a planet inhabited by Viking descendants, in search of allies against the Goa'uld. Upon arrival, O'Neill and Teal'c are trapped in a labyrinth, where the only exit is through Thor's Hammer, a device to destroy Goa'uld, but preserve the host. Goa'uld weapons are rendered inoperative but not earth guns. Also in the labyrinth is one of the Unas, the original host species for the Goa'ulds.

SG-1 goes to Heliopolis (PB2-908) and recovers Dr. Ernest Littlefield, who went through the Stargate in 1945 (using a standard diving dress as a spacesuit) and never returned. Daniel nearly stays behind to study a 'book' detailing the meaning of human existence, left behind by the Four Great Races.

Teal'c's son Rya'c is to be implanted with his first Goa'uld larva on Chulak, so SG-1 goes to prevent it. However, Rya'c falls ill and can only be saved by a symbiote. Teal'c donates his own, and receives a stolen one for himself. The team also meet Teal'c's first teacher Bra'tac, formerly the greatest of all Jaffa warriors and now still a spry 133 years old, who had taught Teal'c that the Goa'uld were false gods.

On P3X-866, SG-1 is given a false memory of Daniel's death by his alien abductor Nem. Nem is a member of an amphibious species named Oannes (Ohne), and wants to know from Daniel what happened to his mate Omoroca in ancient Babylon. Ultimately, Daniel remembers the obscure fact from his studies of ancient myths, and is allowed to go home.

The Goa'uld Hathor (one of the mothers of all Goa'uld) brainwashes the men of the SGC with pheromones, and nearly makes O'Neill host to a larval Goa'uld conceived with Daniel. She flees after the unaffected women of Stargate Command retake the facility.

On the planet Hanka (P8X-987), SG-1 finds the entire planet's inhabitants and SG-7 dead except for Cassandra, a small girl who turns out to have had an inoperable Naqahdah bomb put in her by Nirrti to destroy the SGC. Ultimately the girl is given to the care of Dr. Janet Fraiser, the SGC doctor, after they discover that the bomb will dissolve if she is kept away from the Stargate.

The Byrsa, human inhabitants of the planet Cartago (P3X-1279) that was once enslaved, condemn Teal'c for the atrocities he once committed under Apophis. He is sentenced to death, but when the Goa'uld attack, Teal'c saves his accuser's life and proves he is a changed man.

SG-1 rescues a group of highly advanced Tollan from their homeworld, P3X-7763, which has experienced catastrophic volcanic eruptions. The military and the NID take an interest in their technology, and attempt to imprison them for research purposes before Daniel helps them take refuge with the Nox.

Carter and O'Neill are stranded on an icy planet when the Stargate malfunctions on their return journey to Earth. However, it turns out that they have merely been redirected to a second Stargate in Antarctica.

11,000 years ago, the inhabitants of the planet On Altair (P3X-989) were forced underground by deadly radiation, and eventually transferred their minds into exact android duplicates to survive. By the time SG-1 visits their planet, there is only one remaining individual, Harlan, who creates android replicas of the Earth team to aid him. When this is discovered, the androids must accept that they will stay off-world, and the real SG-1 returns home.

On P3R-233, Daniel finds a strange alien mirror and is transported into an alternate universe where he finds things are slightly different from his own reality, including a Goa'uld attack on Earth. Before he returns to his own reality, he learns of a Stargate address where the attack originated.

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 the danger for Earth as a whole outweighs everything convinces his colleagues to ignore Hammond's command and dial the address tthat he 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.