SG-1 and Jack O’Neill attend a Tok’ra extraction ceremony for Ba’al, the last of the Goa’uld System Lords. Ba’al claims, however, that he is merely the last clone and that the real Ba’al has a fail-safe plan. The real Ba’al travels back in time to 1939 Earth and massacres the crew of the Achilles, the ship carrying the Stargate to the United States; the captain lives long enough to drop the bomb Ba’al left overboard and keep the ship from being destroyed. In the present, people and objects start disappearing, including Vala Mal Doran and Teal’c. Jack is killed by the clone, but Samantha Carter, Daniel Jackson and Cameron Mitchell reach the Stargate. They are surprised to emerge inside the derelict Achilles, which has drifted to the Arctic — Ba’al’s actions have created a timeline in which the Stargate Program never happened. After escaping from the sinking Achilles, they are rescued by a team led by Colonel Jack O’Neill. Although General Landry believes their story (after intensive interrogation), they are denied permission to change the timeline. In the alternate timeline, Daniel is still trying to convince people about his theories of the pyramids, Carter died in a space shuttle accident and Mitchell does not exist at all because his grandfather was the Achilles captain. The three are forced by the authorities to lead separate lives, with no contact allowed between them.
A year passes, and SG-1 is called back into action when Goa’uld scoutships appear. Ba’al has brought the other System Lords under his control and now stands ready to conquer Earth, with Qetesh, still residing in Vala’s body, as his queen and Teal’c as his First Prime. SG-1 is brought to President Henry Hayes and General George Hammond, who inform them that, based on SG-1’s accounts, they have recovered the Antarctic Stargate and are excavating the Antarctic Ancient outpost to reach the weapon that saved Earth in the original timeline. SG-1 is sent in F-15s to McMurdo Station to gate to Proclarush Taonas, another Ancient outpost, to retrieve a Zero Point Module to power the Antarctic outpost.
Above Earth, Ba’al’s armada arrives. To the displeasure of his subordinates, the other System Lords, Ba’al announces that he will treat the Tau’ri relatively leniently. Suspicious about Ba’al’s thorough knowledge of Earth, Qetesh betrays him and forces him to tell her everything. She orders the destruction of McMurdo and the Ancient outpost in Ba’al’s name, but she kills Ba’al when Teal’c discovers what she is doing. As Teal’c escapes to an Al’kesh, Qetesh orders the fleet to bombard Earth, while she goes to secure Ba’al’s time machine.
When the Goa’uld destroy the Antarctic Stargate, SG-1 is rerouted to Russia, as the Russians had retrieved the Achilles’ Stargate from the ocean floor. Teal’c arrives at the facility as well, seeking to use the Stargate to reach the time machine before Qetesh. The two sides agree to a truce and get to Ba’al’s time machine: an underground supercomputer connected to hundreds of satellites that monitor solar flares from various stars that could intersect a wormhole created by the Stargate; the flares are necessary for time travel. SG-1 must wait for the right flare in order to journey to the right time, but when Qetesh’s troops attack, they are forced to dial the Stargate to the year 1929 – ten years before their desired target date. Sam and Daniel are killed in the firefight, and only Mitchell passes through the Stargate. Teal’c, mortally wounded, blows himself and Qetesh up. After a decade of waiting, Mitchell stows away on the Achilles and kills Ba’al and his troops when they come aboard through the Stargate.
In the now-restored timeline, SG-1, completely unaware of the previous events, watch the extraction proceed without incident. On Earth, Daniel wonders what Ba’al meant by his fail-safe.
