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.

A solar flare sends SG-1 back in time thirty years to 1969. Captured by military police at Cheyenne Mountain, they escape with the help of a young Hammond and then must find the Stargate so they can return to the present.

An alien incursion takes control of the base.

When Daniel's Unas friend, Chaka, is captured by another world's slavers, SG-1 goes to that world to rescue him.

The Russian SG team brings back a man who claims that his people are being experimented on by Nirrti. SG-1 investigate where the experiments are conducted, with the Russian SG team as backup. The inhabitants worship Nirrti as their god and savior from a terrible plague. SG-1 attempts to use the same device Nirrti used on the people to reverse the mutations, but the people turn on them at the arrival of Nirrti.

The US and Russia reveal Stargate Command and its operations to representatives of the other permanent members of the United Nations Security Council.

When an SG geological exploration mission runs into deadly conflict with an indigenous Unas clan, Daniel gets Chaka to help seek an accord with it.

In exchange for new tech for the SGC, Warrick Finn asks for their help to win a dangerous spaceship competition.

The Tau'ri and Tok'ra have used their captured super-soldier to determine his planet of origin. With Daniel, Dr. Lee, and the Ancient device they found in the hands of Honduran kidnappers, SGC must find a way to retrieve them if they are to have any chance of defeating the newly encountered super-soldiers.