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.

On an astronomical black hole observation mission, SG-1 finds a fatal bacterial mass-epidemic on a planet where the natives told then-incredulous Daniel months ago that the coming solar eclipse would bring disaster. They also take back to the Cheyenne Mountain Base a surviving, fairly healthy, orphaned young girl named Cassandra, and awakes Sam's maternal instinct. The Naquadah traces found in her blood turn out to have made her immune, but after she has a seizure they are diagnosed to constitute a huge bomb, somehow triggered by rescuing her; the whole thing must be planned as a 'Trojan Horse' by the Goa'uld. Sam takes the prospect of sacrificing Cassie personally and is prepared to take personal risks.

SG-11 failed to report regularly while mining trinium, a vital mineral for earth's defense against the Goa'uld. SG-1 finds them missing, and all traces cease at the site of arrow-heads made from trinium. Then they are all sedated by such arrows and brought to the village of Tonané, whose earthly tribal ancestry Daniel identifies by its animal totems. However, they are soon awake and released, their guns even returned, and promised to get their friends back, too, from the wolf spirit T'akaya, and the raven-shaped supreme spirit Xe'ls. The council of elders refuses to allow resuming of the mining, which is disrespectful to nature, but Tonané is delegated to be shown alternatives on earth. Both teams return to SGC, or so it appears; in fact, SG-11 is a series of incarnated spirits, who are soon convinced the earthlings are most untrustworthy.

When the SG-1 team discover a sealed chamber of nine dead Goa'uld, Daniel Jackson is exposed to the parasites that killed them and threaten to drive him insane.