As order breaks down and the project is jeopardized, Jackson and Teal'c head back through the Stargate in an attempt to discover the reason for this mysterious transformation. They know they can't save her, but can they save themselves and Skaara before they're killed by the Goa'uld guards and before General Hammond sends a nuclear weapon through the Stargate to destroy the planet? Daniel discovers common ground with Nem - both have lost their true loves to the murderous Goa'uld - and the key to his freedom. The Nox are a small, peaceful, fairy-like people who occupy the planet previously thought to be uninhabited. But, the Stargate program faces a more immediate threat - - this from Senator Kinsey, powerful Chairman of the Appropriations Committee and the man who oversees Stargate's multi-billion dollar budget. He must find a way back to his reality, but this proves difficult, as in that Universe the are invading Earth and is still '. Skaara was once the young Abydonian friend to O'Neill, but now is the host body to Klorel, son of Apophis. Narim, another Tollan, reveals the reason for Omoc's suspicion.
After dispensing with the scientists, Hathor makes her way to the Stargate mountain facility dressed as a homeless woman. The team members use hypnosis to revisit the events leading up to Daniel's disappearance. Carter and Jackson have discovered that the crystals contain energy beings that can read minds, mimic people and communicate. When they awaken with seemingly no ill-effects, they hastily return to. More mysteriously, they seem to age very rapidly - a lifetime is 100 days - an effect that O'Neill unwittingly inherits when he is seduced by Kynthia, a stunning Argosian woman. But, the team can't figure out how to turn them off, and unless they can, O'Neill will soon be dead. As the goddess cooks up thousands of Goa'uld larvae and prepares O'Neill to bear one, it falls to Carter and the handful of women at the base to fight back against the powerful seductress.
It is also clear that these aliens are not from Abydos. The Nox can make things invisible - it is they who shield the A'kasha a flying insect-like creature from the sight of the hunters - and bring back the dead. The government, however, has other plans as evaluates the dangers of the. After Daniel delivers the child, the team is invited to a festival, where they find a civilization of beautiful, happy people who celebrate while the sun shines and mysteriously drop to sleep the minute that it sets. To make matters worse, Kawalsky, O'Neill's right-hand man, has been having terrible headaches caused by an alien larvae that has attached itself to his brain. The Gate is a large ring consisting of an alien element called Naquadah.
Once inside, she uses her physical charms and a drug-like pink smoke to seduce the men and enlist them in her plan to take over the world - - using O'Neill as her first Jaffa. There they discover that Sha're is now Apophis' queen; her body has been taken over by the hideous snake creatures, known as Goa'ulds, who rule this planet and collect life forms from around the galaxy to use as hosts. Samantha Carter, who takes a back seat to no man, is threatened by death on her first encounter with the Shavadai chief, Mughal, and is only spared because she saved the life of his son, Abu. O'Neill and the team offer to defend the Nox against Apophis, but the peaceful little people have their own solution, far beyond the understanding of either Goa'ulds or the people of Earth. Meanwhile, a revived O'Neill returns through the gate, only to realize he's been replicated. Despite being told by Teal'c not to interfere, does not want to go along with the process.
Soon, with all the males loyal to her, it is up to the females of the base to stop Hathor before it's too late. They find themselves on a Goa'uld ship, full of Jaffa warriors, traveling through space at many times the speed of light. Hathor is a Goa'uld who has taken on the persona of a powerful Egyptian goddess, awoken from a sleep that has lasted a millennium. Carter grows especially close to Cassandra and is shocked when she discovers that the chest pains Cassandra is experiencing are caused by a metallic device growing around the child's heart. They are constantly confronted with new civilizations and dangers.
He touches the mirror and gets a mild jolt but thinks nothing of it until he returns through the Stargate. Their theories turn out to be correct, when Jackson is actually imprisoned by an named to extract information regarding the whereabouts of his mate,. The Touched, who live on the dark side, are heavy-browed primitives with limited skills and the brutal instincts of animals. Davis, Peter Williams, Jay Acovone. Now, however, his son Rya'c has reached the age at which he will receive his Gou'ald larva, and Teal'c is determined to stop the process that would make his boy a servant to the Gou'alds. The only way to cure them is to get a blood sample from the , who believe the disease to be a curse. She begins to exert her influence on the men of the base in order to start building her new army.
But, Daniel Jackson and Teal'c may have the best solution; with the help of Jamala, one of the planet's inhabitants, they set out to show the people of the planet that Hanson's power comes from technology - - not divinity. As they marvel, however, the aliens led by the handsome but evil Apophis, are making use of a similar map. Kinsey sees the program as a wasteful fat cat with dubious goals and he vows to shut it down. They emerge from the Stargate on Abydos, and after a brief battle, kidnap Sha're and Skaara. He is called back to duty by General Hammond when a group of aliens emerge from the Stargate, kill the soldiers guarding it and kidnap a female guard. It allows to travel with virtually no loss of time through the universe. The team gathers up a few survivors and returns through the gate to Earth.
O'Neill is reunited with his old comrades Kawalsky and Ferretti and joined by Capt. When they return to Earth, over Harlan's objections, the team members discover what he means. Upon their return, they confront Harlan, who, as a robot himself is mystified by their demand that he put them back in their human bodies and sacrifice their immortality. Meanwhile, finds his family and tries to keep his son, , from being implanted with a symbiote. Daniel and Carter ascertain that the Goa'uld planted the device as part of a scheme to destroy the Earth's Stargate. There, they discover that they've been turned into. The labyrinth is home to Unas, a vicious creature that is the original Goa'uld host, but it is also Thor's Hammer, which is designed to kill Goa'ulds.
The double explains that he never meant to hurt O'Neill. Carter to try to dig the nearby gate out of the ice and find a way to make it work. The two nevertheless attempt to find a way out, but are found by an unwanted visitor who will stop at nothing in killing them as it attempts to escape. With little time remaining, the only way to save him is by careful and potentially life-threatening surgery to remove it. But the reunion for Littlefield and Catherine is bittersweet and things are further complicated when the is destroyed in a storm, forcing the team to resort to drastic measures in order to return to Earth. O'Neill faces-off against Teal'c, who in this reality is still loyal to the Goa'uld, and Daniel tries to escape through the Stargate with information that may save his world from the fate of this alternate reality. They are revived, along with Shak'l, a Jaffa who was also killed in the battle by the Nox.