It's a normal day at Stargate Command and SG-1 reports to the Gate Room for their mission, as Landry bids them goodbye. He informs the team that Colonel O'Neill has gone ahead with SG-3 to deliver the prisoner, Ba'al, for symbiote extraction. Vala shows up, carrying a big gun in anticipation of execution, and they take it away from her. Vala talks about the experience of undergoing extraction, while Mitchell notes it's his first extraction.
SG-1 arrives on the Tokra home world where Ba'al is being held for the ceremony as they chant all of his crimes for the last three hours. Vala suddenly disappears but before they can pursue the matter, Ba'al is called forward and given the chance to speak his last words. He addresses himself to SG-1. He expresses regret that Teal'c didn't become his First Prime, and then notes that Vala has disappeared. He then informs them they've made a mistake and hints he's not the last clone. Ba'al boasts that even though they think he's the last, he has a failsafe in place but they don't believe him.
In the Atlantic Ocean, the freighter Achilles is dodging U-boats and carrying a mysterious cargo. The ship starts to shake and the captain sends his mate down to the cargo hold to check the cargo: a large crate addressed to Catherine Langford. The device inside the crate is making noises and suddenly a wormhole expands outward from it, through the side of the ship. As the captain goes down to investigate, Ba'al and Jaffa emerge through the Stargate and secure the ship.
Michael is still looking for Vala as Ba'al is prepared for extraction. Suddenly Teal'c disappears as Ba'al chuckles. The Tokra start disappearing as well and Jack confronts Ba'al, who stabs him with an extraction needle. Mitchell shoots Ba'al while the others go to Jack, who is dying from the poison in the needle. With his dying breath he tells them to get to the Stargate. Ba'al disappears as well as they leave.
The Jaffa attack and kill the crew, injuring the captain.
Mitchell collapses, weakened.
As the Jaffa take the bridge and kill the radio operator, the injured captain slips away. Ba'al dials a new address on the Stargate as the captain slips into the cargo hold. Ba'al uses a one-shot power device to power it, steps into the wormhole, and disappears. The wounded captain finds a spherical object that the intruders left behind. He throws it through the hole in the side and it explodes a minute later as the freighter continues on its course.
Mitchell, Daniel, and Sam get to the Stargate as the Tokra city disappears behind them. They go through the Stargate to Earth and find themselves aboard the freighter, now covered in ice. Mitchell gets Sam to snap out of her shock at seeing Jack killed and they determine the temperature is dropping rapidly. There's no DHD and no EM signal. Daniel finds a life jacket identifying the ship as the Freighter, the ship that delivered the Stargate to America. Mitchell thinks the name sounds familiar for another reason but can't identify it. With the temperature dropping to danger levels and no way to start a fire, Mitchell shoots a hole in the ice and plants explosives, then sets off the charge. They blast a hole to the ceiling, but the ship is dislodged from the ice and starts sinking. Mitchell finds some cold weather gear and they get to the surface as the Achilles go down. Daniel is suffering from frostbite and tells the others to leave him to go get help.
Sam and Mitchell reluctantly leave him and make their way across the Arctic landscape. The next day they run into two snow-clad military figures: one is Colonel Jack O'Neill. He recognizes Sam but believes she's an astronaut who died years ago. He takes them to a nearby submarine, the USS Alexandria, and takes them to the ward room where Daniel has already been recovered. The submarine medic is forced to amputate his frostbitten leg. Jack explains that a satellite detected the wormhole when the Stargate activated. They try to explain to Jack what happened but he is skeptical of their story. When Daniel tries to prove he knows Jack by talking about his dead son, an angry Jack notes that his son is alive and well.
The three SG-1 members are taken to an Air Force base where they are interrogated at great length and forced to repeat their story over and over again. General Landry finally comes to see them and informs them that he believes their story. They have no record of Mitchell (although his grandfather, a Merchant Marine, died in 1939), Sam died several years ago sacrificing herself to save her space shuttle crew, and Daniel Jackson is a crackpot exploring ancient pyramids for signs of alien interference. Landry as no intention of letting them restore their original timeline: doing so would wipe out everyone in the existing timeline. Sam warns that Ba'al is up to something but the general notes that there's no sign of him. She warns that Ba'al is probably reestablishing his power base but Landry is skeptical. He informs them that they will be given new identities and forced to live separate lives. They may be called upon as consultants but they'll never be allowed to go through the Stargate again.
One Year Later
Sam, Mitchell, and Daniel are settling into their lives as best they can. Mitchell goes to visit his family farm, while Daniel discovers his counterpart's book. He calls his counterpart without identifying himself and tries to tell him that his theories are right. His counterpart hangs up on him.
Alkesh vessels soar over the cities of Earth and Sam and Mitchell both learn of the alien scout ships. They contact Landry, who brings them to an underground bunker to meet with President Henry Hayes. The team warns the President that the Alkesh are just the advance scouts and Ba'als fleet is on its way. Hayes asks them for ideas and they suggest that they use the Ancients' Antarctica weapon platform and the second Stargate. Hayes informs them that he's already had the Army Corp of Engineers digging on the southern continent and they're close to both objectives. Sam warns that they'll need a ZPM to power the weapon platform and Hayes okay their mission to recover one. He assigns them a military escort to keep them safe, and make sure that they don't try anything to restore their timeline.
Ba'al's fleet arrives in orbit above Earth. He has captured Apophis, the last of the System Lords to resist him. Teal's, now serving as Ba'al's First Prime, bring Apophis in and Ba'al executes him. Ba'al then goes to his throne and sits beside his queen: Quetesh, in Vala's host body. Quetesh is impressed by how Ba'al has foreseen every possible difficulty, and kept his promises to his allies such as Teal'c. Ba'al has secured Teal'c loyalty and that of the Jaffa by promising them a free nation. The System Lords who have allied themselves with Ba'al arrive and one of them, Camulus, questions Ba'al's intent to keep his word. In response, Ba'al forces Camulus to give up half of his future Australia holdings to Teal'c. Ba'al then orders the System Lords to hold their fire, as he plans to use diplomacy to convince the Tau're to ally with him. Only when it's too late will they realize his plan to turn them into servants for the Goa'uld. Meanwhile, Ba'al learns that the Tau're are busy at Antarctica and orders Teal'c to destroy the engineers working there.
Mitchell, Sam, and Daniel, along with their fighter escort, head out but get word that the Antarctica base has been destroyed. Hayes gets word from the Russian Premier that they have an artifact, and he tells SG-1 to head for Russia and do whatever they need to do. Ba'al calls President Hayes via cell phone and offers to meet peacefully with him. Hayes is skeptical but agrees to an initial meeting. After Ba'al signs off, Quetesh demands to know how he knows so much about Earth despite the fact she has been at his side for years. She then skewers him with a short sword, demanding that he tell her his secrets. He refuses, and Teal'c enters the room. Despite Quetesh's efforts, Teal'c realizes that she is usurping the throne and runs. Quetesh kills Ba'al and his symbiote and chases after Teal'c, killing his warriors. However, she's unable to stop Teal'c before he teleports to his personal vessel and put up the cloaking field. Quetesh orders the other System Lords to begin bombarding Earth into submission and heads for Praxion, Ba'al's base of operations. Realizing where she's going, Teal'c resolves to avenge his lord but needs a Stargate to get to Praxion first. He has his crew start scanning for a Stargate on Earth.
The fighters are crossing the Atlantic when Goa'uld fighters intercept them. The escort fighters hold them off long enough to get near Russia where MIF fighters come to their aid. SG-1 lands at the Russian research base. One soldier greets them: the others have left to be with their families. They convince the soldier to take them to the artifact: the Arctic Stargate, which the Russians have recovered. However, there's no power source. As they try to come up with a solution, Teal'c lands his ship atop the building and extends the force field to protect it. He comes down and SG-1 holds him at gunpoint. They offer to help him defeat Quetesh but need his help, so they offer an alliance. Teal'c agrees and provides a power device for the Stargate. The System Lords begin to bombard the facility and they manage to escape through the Stargate just in time as the building comes down around them.
The group arrives at Ba'al's base on Praxion, which contains the time travel device which he created. The device tracks solar flares throughout the galaxy and is capable of directing a wormhole into their magnetic field to reach precise times. Sam begins to decipher the mechanism as Quetesh arrives in orbit above and Jaffa start beaming into the chamber. Mitchell, Daniel, Teal'c, and the Jaffa fight a holding action while Sam tries to find the precise solar flare that they need. The closest one she can find is one that will take them to 1929. Quetesh's Jaffa pick off their opponents one by one: Daniel goes down, and then Sam is killed just as she activates the wormhole to 1929. Teal'c hold off Quetesh's Jaffa long enough for Mitchell to dive into the Stargate, then he's shot down as well. Quetesh arrives to gloat over her fallen foe, but the mortally wounded Teal'c declares that he'll die free... and activates a bomb, destroying everyone along with the base.
In the Atlantic Ocean, the freighter Achilles is dodging U-boats and carrying a mysterious cargo. The ship starts to shake and the captain sends his mate down to the cargo hold to check the cargo: a large crate addressed to Catherine Langford. The mate finds a bearded man waiting for him: Cameron Mitchell. Mitchell has several rifles and gives one to the mate, and they set an ambush. The wormhole expands outward through the side of the ship and Ba'al and his Jaffa come through. Mitchell and the mate gun them down, putting a bullet in Ba'al's head for good measure. The captain comes down and wonders what happened, and he and Mitchell look out on the ocean.
Jack and SG-1 watch as Ba'al undergoes the extraction process. His Goa'uld symbiote is removed and the Tokra destroy it and declare that the last System Lord is dead. The team wonders what Ba'al meant by his earlier threats. Jack offers to buy everyone lunch and Vala chooses to remain with Ba'al's host to help him acclimate to life without a symbiote.
Back on Earth, Mitchell, Daniel, and Teal'c are preparing to head out for lunch as they consider Ba'al's last words. As they leave, a photo in Mitchell's locker can be seen: Cameron, with his grandfather.