The team, now designated SG-1 are planning their next foray through the gate as they try to map out the variety of sites available to them and locate their missing friends. O'Neill asks that Teal'c be allowed to join his team but Gen. Hammond thinks that will be unlikely given that he is the host for a Goa'uld. Unknown to anyone, however, is that O'Neill's close friend, Maj. Charles Kawalsky, leader of SG-2, has been infected by a Goa'uld, an immature version that has not yet taken complete control of the host. Kawalsky is having regular blackouts during which the Goa'uld is trying to return to the gate. An MRI reveals what is wrong but it's unlikely the creature that has fused itself to Kawalsky's spine can be surgically removed. Meanwhile, Col. Kennedy arrives to question Teal'c who has pledged his loyalty to his new world.

While exploring a world populated by Mongol descendants, Capt. Carter is abducted for a wife of a local warlord.

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.

SG-1 has to deal with a Replicator infestation on a Russian sub on Earth while Major Carter advises the Asgard about combating the menace in their galaxy.

When SG-1 flees from an expedition with Col. O'Neill and some mysterious team member named Tyler, whom no one else knows about, stranded, the fitness of the team is questioned.

Stargate Command gets a video message from Vala's extremely unreliable father, Jacek, on the planet Robak; he claims to know about the late Arkad's plans to attack and blow up Earth, even about the several cloaked, Naquadah-laden cargo ships in orbit, and offers details in exchange for sanctuary. General Landry asks Dr. Lam to help him resume contact with her mother, Kim, his ex-wife. Even after the cargoes are found and blown up, Vala abhors her dad's entry. The general asks her to go easy on him, realizing that he, too, neglected his daughter because of his career, even if Jacek's neglect was just criminal. When Cam and Daniel go tell Jacek he shouldn't scam people, he tricks them into talking to Vala for him. Vala goes over just for catharsis, telling him she's through picking up the pieces of his tricks, and he certainly keeps scamming - as Daniel also finds - even with Terak, a Jaffa from an escaped cargo ship, who hopes to sell the Naquadah. When they are apprehended, Jacek promises to help track it and override the rigging of the cargo ship. The Jaffa wait for Jacek and Vala, intending to eliminate them now that Terak is gone, but SG-1 saves them. Since there never was an override, Jacek cheerfully flies away alone in the cargo ship, ignoring that his treachery was anticipated: it's a decoy.