The Stargate team must justify the project's continuation when a doubtful senator, Head of the Congressional Military Appropriations Committee, comes to review the project's performance.

General Hammond mysteriously retires from the SGC and a new general is brought in, who breaks up SG-1: Daniel and Sam are scientists, Teal'c is with SG-3 and O'Neill commands a new SG-1. O'Neill tries to convince Gen. Hammond to return, but he finds out that someone ordered Hammond to leave or they would hurt his grandchildren. While the others are occupying the new general, O'Neill tries to find out who that "someone" is. Thereto he must place his trust in the one person he hates most: Maybourne.

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.

SG-1 makes contact with the Aschen, unaware of that their homeworld is one they were warned previously from the future to be considered off-limits.

Senator Kinsey is shot in the chest at a public event, killing him just before his party's presidential nomination. Jack is arrested for the murder, and General Hammond assigns the rest of SG-1 to uncover the truth.

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

The president has asked that a documentarian go to SGC to create a film about its operations. His arrival is unwelcome to most and he begins to clash with the base personnel. Nevertheless, he conducts his interviews with SG-1 and the scientists in the employ of SGC. Meanwhile, an off-world SG team finds the remains of an Ancient city.

The newly inaugurated President of the United States is briefed by the Head of the Joint Chiefs of Staff on the Stargate program. Former Senator, now Vice President, Kinsey attempts to get his running mate to back his policies for the program, but the president decides to look into the situation himself. Kinsey gets Richard Woolsey to convince the president of his agenda.

Vice President Kinsey briefs Dr. Weir on the Stargate program before her meeting with the president. SG teams 1, 3, and 5 go off-world to attempt the extraction of a newly found Ancient repository device. Upon arriving at the location of the device, SG-1 comes under fire from Goa'uld ships. With no other way to disallow Anubis from claiming the knowledge for himself, Jack submits himself to the dangerous device.

With Jack having the knowledge of the Ancient repository once again in his mind, he and Daniel attempt to unearth the location of the Lost City of the Ancients. Bra'tac, bringing with him the news of an impending attack on the Tau'ri by Anubis, takes Teal'c to help him acquire ships and warriors for the defense of Earth. Dr. Weir attempts to cope with the overwhelming nature of her new job, while also dealing with the unrelenting ego of Vice President Kinsey.

Ex-Vice President Kinsey comes to Jack informing him of the Trust's activities including what seems to be a plan for the Russians to reclaim the Stargate they lent to the United States. He decides to use Kinsey as their inside man with the Trust. Kinsey wears a wire for his meeting with the Trust to set up a meeting with a high-ranking Russian general. The plan goes south when the signals get jammed just as the Trust makes an astounding revelation to Kinsey and they beam out.