The SGC is preparing for the Goa'uld attack. America's best and brightest are sent through the Stargate to a safe Alpha site on a different planet. Back on one of the Goa'uld ships, SG-1 are trying to blow them up. They are aided by Master Bra'tac who was Teal'c's Jaffa teacher. They realise that they don't have much time, and when Daniel is shot they put him in a sarcophagus and leave before the ships blow

After coming back from a mission to rescue some survivors of a planet attacked by the Goa'uld, Cassandra (season 1 Singularity) notices that a Goa'uld is now in Sam's body. Sam is put in a cell but the Goa'uld within her tells them he is a Tok'ra - a sect of Goa'uld who disagree with the bloodthirsty ways of the System Lords. However, they don't get much time to trust her as an Ashrak was with those which were saved, and an Ashrak is a Goa'uld assassin sent to kill the Tok'ra named Jolinar.

SG-1 accidentally break the law on a planet they are visiting by saving a man who seems innocent enough however has committed a crime and ran. The race which resides there do not tolerate crime, and send even those who help criminal to prison, which is a penal world where only the strong survive. There they meet Linea a woman that all the prisoners fear, she seems to be the key that will help them to escape, as long as they take her with her.

Daniel becomes entangled with a princess when he saves her as she tries to commit suicide. By rescuing her he and the rest of SG-1 are captured and made to work in a mine. When Daniel is injured during an escape attempt the princess revives him in a sarcophagus. The rest of the team are still working in the mine as prisoners while the princess seduces Daniel and corrupts him with the sarcophagus.

SG-1 return to Cimmeria to discover that the Heru'ur one of the Goa'uld System Lords has invaded the planet. They feel responsible as they destroyed "Thor's Hammer" which defended the planet from the Goa'uld by taking them to a labrynth where the Goa'uld within them was killed. Offering to help Sam and Daniel go with Gairwyn to look for the Hall of Thor's Might, there they discover a hologram of Thor who has various tests for them. Meanwhile Teal'c and O'Neill try guerilla warfare however, when they see the huge army of Heru'urs' they see that it would be too hard. However they are saved when Thor comes and saves them.

Exploring a now-dead planet SG-1 find an orb which they think is a time capsule. However when they return to Earth they realise that they are wrong and decide to return the device back to the planet, however when they try to take it through the stargate, the device extends and halts movement by hooking itself to the floor and onto Jack through the shoulder. After a while it appears to infect the whole of SGC. SGC gets quarantined to protect the rest of Earth.

Master Bra'tac comes to tell Teal'c that looking for revenge Apophis has kidnapped Teal'c's son, Rya'c. Teal'c, Bra'tac and the rest of SG-1 go to rescue him. Unfortunately when Teal'c goes to rescue him, he realises that Apophis has brainwashed him into believing that Apophis is a god. He also implants a bomb into Rya'c so that once he is in the SGC Rya'c can activate the bomb and take down the SGC. However, once Teal'c brings him back to the SGC, Dr Fraiser finds the bomb and is able to take it out. However, Rya'c is still under the control of Apophis.

However he is saved when Teal'c decides to shoot Rya'c with a Zat gun which seems to bring him back to his sense.

Daniel Jackson and Teal'c return to Abydos to fulfill a promise Daniel made to Sha're's father, Kasuf. Once there they find Shar're, and she's not only pregnant, she's very near to giving birth, for the time being the Goa'uld within her is dormant and she is the Sha're Daniel loves.
Back on Earth Sam and Jack are to get medals from the President but Jack has problems with a reporter and Sam discovers some disturbing news about her father.

On Abydos, Sha're is about to give birth, however, when before she can Heru'urs' forces come to find the baby and use its knowledge to kill Apophis. However, Teal'c manages to save the baby from them, but as soon as the baby is born Sha'res' Goa'uld takes over. As they try to escape through the Stargate, Apophis appears and Sha're tells him that it was Heru'ur that took the baby, but as they leave she sees Teal'c and Daniel however she does not reveal their positions.

On BP6-3Q1, SG-1 are attacked by giant insects. Teal'c is stung and after returning to Earth Teal'c's DNA starts changing. When Simmons tries to get him transported into a more secure location for observation, Teal'c manages to escape mid-way and with the help of a girl finds shelter. In the meanwhile, Dr Fraiser is trying to find a cure, and realises that Teal'cs transformation will be speeded up without his Symbiote which he left on the prison transport.

SG1 go back to the planet and try to capture another creature so they can study it and find a cure. Once the creature has been caught Dr Frasier is able to conduct a remedy, however, without Teal'c present they cannot save him. However, the little girl is able to contact the SGC and give them the location of Teal'c. Jack and the SG team rush to save him and are able to cure him of the transformations.

Using the latent knowledge Carter has from her dead Tok'ra host, SG-1 go to find more of the Tok'ra to see if they want to become Earth's allies. The Tok'ra are a bit suspicious, can Carter help allay their concerns? Carter is also worried about her dad who's dying of cancer, and once with the Tok'ra she discovers why Martouf (one of the Tok'ra) seems so familiar.

The Tok'ra turn down the request for an alliance, they feel Earth does not have enough to offer, no one is even willing to host Selmak, a Tok'ra who's host is dying. Carter has an idea, her dad is dying of cancer might he be willing to be Selmak's host? While he is being fetched the Goa'uld find out where the Tok'ra are and attack. However, with the help of the SG team, they are able to save themselves as well as the Tok'ra Selmak, who is now inside of Jacob.

When Trinium, a metal 100 times lighter and stronger than steel, is discovered on a planet inhabited by a race that seem to be related to American Coast Salish Indians the SGC decide to mine there to get the supply. However, these people are protected by "the spirits", who also give them the metal trinium. One of the Salish, Tonane returns to Earth with SG-1 to negotiate a mining treaty, however he rejects the offer, and the SGC decide to go mine it anyway without them knowing, even though SG1 are against it. However, when the Spirits find out they are not happy and decide to punish them, and start making the soldiers on the base disappear. However, the SG team are able to make Tonane and the Spirits understand and they bring back all those that disappeared and they decide the bury the gate so they can't come and mine behind their backs.

A team posing as a SG team steal a weather control device from the planet Madrona, which SG-1 have previous contacted. When they go to the planet to take a look at the device they realise what has happened and that someone has stolen the device. The weather deteriorates and threatens the inhabitants with death. On Earth strange things start happening with the weather. SG-1 team realise that the device is on Earth and that the Stargate which was found in Antarctic which was sent to Area 51 has been switched with a fake.

They find the location of the gate and get it back along with the device, however they are unable to capture the people that stole the gate as they dial out and run before SG team have a chance to stop them.

O'Neill accidentally gets a brain full of the knowledge of an alien race, but it's too complex for the human brain. Alien words start appearing in Jack's speech and soon his entire brain seems to be taken up with the superior knowledge of the Ancients. However with so much information to handle Jack seems to be dieing unless they can find a way to get the information out of his brain. However, under the influence of the Ancient knowledge, Jack is able to save Sam by helping them repair a DHD on a planet in which the Temperature is rising very fast, and also adds a large number of gate addresses to the database. Jack also creates a device which seems to be a sort of power source and uses it to dial to a 8 glyph address, a planet which is located in another galaxy. General Hammond reluctantly lets him go, as Daniel realises there's not really anything they can do to stop him.

Once on the other side Jack meets with the Asgard who are able to remove the information from his brain and send him back to Earth.

SG-10 become trapped on a planet while observing a black hole. The intense gravitation of the black hole is affecting the gate, and all of SGC, making time slow down, and they can't close the gate as the gate starts to draw power from the other side. When they realise that unless they shut the gate the planet would be destroyed, they decide to destroy the base and hope that it will destroy the gate and shut down the wormhole.

A Badly injured Apophis asks SGC for sanctuary as he is dying and promises all the Goa'uld knowledge in return for a new host body, however the SGC refuse him. Martouf of the Tokr'a tells them that Sokar is after revenge against Apophis and unless they send him back to face his fate, Sokar will destroy them all.

However, it seems too late when Sokar starts an attack against Earth by sending particles which increase the radiation and heats up the Iris, and unless the attack is stopped they will be killed. However, when the wormhole disengages after the 38 minute gap, whilst they try to dial to the Planet to send Apophis back, Sokar dials in first and starts the attack again.

Sam then creates a program which would allow them to dial a lot faster and hopefully before Sokar can dial in. When the gate shuts down they are able to dial the gate and send Apophis through. They are relieved that the Sokar stops his attack.

SG-1 seem to have caused a plague among a friendly, gentle race. Can Dr Fraiser help find a cure before they all start dying?

A young boy comes through the gate, despite the Titanium iris. He tells SG-1 he's come with his mother, a member of the invisible Reetou race. They've come to warn Earth that Reetou rebels, after having their planet destroyed by Goa'uld, want to kill all humans. Their flawed reasoning being, that the Goa'uld need humans for hosts therefore without humans no more Goa'uld. As the boy bonds with Jack he explains that his mother "made" him so he could act as an intermediary between the Reetou and humans. Tragically the boy is dying, and when Jacob (now of the Tok'ra) comes with a Tok'ra device which makes the Reetou visible they discover that some Reetou are already in SGC.

Waking from cryogenic suspension, Jack is told he's been frozen for 79 years and the rest of SG-1 died long ago. He was returned through the gate already frozen and they use a device which can project his memories holographically as they want to find out who helped him to survive all those years ago, as they might be able to help them in their war against the Goa'uld.
O'Neill becomes suspicious when he hears the Doctors talking in Goa'uld, and he escapes, to find Daniel and Sam near by, in a similar situation to him. Trying to escape they realise they are in a Goa'uld stronghold, but which Goa'uld and how to get home?