Colonel Jack O'Neill is brought out of retirement to lead a new expedition back to Abydos, only to find an old friend, a new enemy and a far wider use of the Stargate.

In 2010, Robert Kinsey is president of a brave new world since he concluded the alliance with the Aschen, a race discovered by SG-1 which lets humanity enjoy its far advanced science and technology, including a vaccine against aging. Sam is now a civilian scientist, married to ambassador Joe Faxon, whose only worry is failing to get pregnant. When she double-checks the Aschen doctor Mollem's computer with Dr. Fraser, who felt superfluous given superior medicine, they discover human fertility is down 90% worldwide in three years. Sam, Daniel and Teal'c turn to retired general Jack, who always warned against handing over technological control, for a daring plan to turn the clock back like general Hammond did once, sending a message to their past with the exact time of a solar flare, which Sam can calculate using the Aschen computer. Only one ingredient is out of their reach: the GDO device to control the Stargate's iris, which is in the White House. Sam implores her husband Joe to steal it, but he has a secret as well as sincere objections.

A new leader has risen among the Free Jaffa, K'tano, former First Prime of Imhotep. SG-1, accompanied by Bra'tac, seeks an alliance between the Tau'ri and the large force he has amassed.

While still dealing with the loss of Daniel Jackson the SGC is contacted by the Asgard who require assistance dealing with Anubis, who seems to have new shield technology that can repel Asgard weapons.

The Tok'ra are forced to evacuate their newly established base under attack from the Goa'uld. They flee to the SGC's Alpha site. Tensions rise between the allied factions, the Free Jaffa, Tau'ri, and Tok'ra. Jacob and Selmak feel the end of the Tok'ra is near and Sam finds a Naquadah generator has been sabotaged to function as a bomb. Jack suspects the recently arrived Tok'ra and attempts to weed out the traitor.

The discovery of the Stargate creates a war between two nations on the planet Tegalus with Daniel in the middle of it.

Teal'c is unhappy with his son's plans to marry. Ishta arrives bringing news that Hak'tyl may be compromised. Complications arise when O'Neill allows Hak'tyl to inhabit SGC until a new homeworld is found for them.

SG-1 is sent to warn Harry Maybourne that the goa'uld System Lord Ares is coming to the planet where he was banished, and in the process they find what may be an Ancient time machine.

Leader of the Hak'tyl and their representative on the Jaffa High Council, Ka'lel has fallen in with those who work against a democratic Jaffa nation. Things worsen when she incapacitates and turns a well-spoken brother Jaffa who promoted democracy. Bra'tac comes to Hayes and SG-1 for help in finding a now missing Teal'c and uncovering the shadowy dealings in the Jaffa High Council. On Earth, Mitchell gets an old friend of his into a hospital where alien-based technology is used; hopefully, the advances they have made will be able to cure what ails him.

When SG-1, minus Carter, investigates a previously unexplored planet expecting to find themselves in a pyramid, they are astounded to find themselves in a museum. Finding a party occurring in the lobby, they decide to leave and make first contact later, but they find that the DHD is a replica and thus incapable of getting them home. They are discovered and believed to be rebels and are forced to take hostages to buy time for their escape.