The alternate SG-1 must go back to ancient Egypt to correct the past. They meet the original timeline Daniel who is the only survivor of a failed rebellion against Ra. Together, they must formulate a plan to steal the Stargate so that Ra cannot take it with him.

SG-1 and General O'Neill use the time traveling puddlejumper to go to Ancient Egypt to recover a ZPM. They successfully steal it, but something is wrong and the future is altered to that the Stargate program never happened. Daniel, Sam, and Jack must find a way to save their reality despite never having met before.

While Daniel finds himself in a mysterious diner suspended between death and ascension, Jacob's fate takes an unexpected turn, Jack and Sam consider their romantic lives, and Anubis unleashes his plan for galactic destruction.

Ba'al sends his fleet back to retake the planet Dakara, pitting his ships against Teal'c and the Jaffa. The RepliCarter tries to probe Daniel's mind to find all the Ancients' knowledge, while Jacob and Carter discover the Ancient weapon on Dakara and try to figure out how to use it to destroy the Replicators.

The Replicators threaten to overwhelm the galaxy, taking out the Goa'uld and then Earth. While Sam and Thor work to develop a weapon, Teal'c and Bra'tac lead the rebel Jaffa in taking a major temple and Jack and Jacob are forced to make an alliance with Ba'al.

Jack is confronted in his home by an irate barber who claims to know everything about the Stargate project and SG-1.

Robert Kinsey contacts General O'Neill and tells him that the Trust is trying to bring down the U.S. government, and want Kinsey's help. Kinsey and the Trust escape surveillance but when the trail leads to Russia, Daniel is captured when it is revealed that Kinsey tried to kill a leading Russian general.

The planet that Harry Maybourne was relocated to by the Tok'ra is targeted by a System Lord and SG-1 must go to rescue him. They discover that Harry has made himself king using knowledge of the Ancients--knowledge that may give them access to the Ancients' time-travel technology.

A Kull warrior manages to ring aboard the Proetheus on its way to Atlantis. It rings all of the crew off the ship except for Daniel, who must deal with the Kull warrior when he is left alone on the ship with it.

The Replicator Carter that Fifth created contacts the SGC and tells them that she wants to be destroyed. She also tells them that Fifth has made all Replicators immune to the disruptor. But does she have an ulterior motive...?

The Trust is behind a plan to steal the Stargate and eliminate the Jaffa and the Goa'uld with the Tok'ra poison.

Teal'c is upset when his son Rya'c plans to marry a Jaffa woman of the Haktyl who he sees as not fit for him. Meanwhile, the Haktyl have been compromised, and Ishta is forced to move her people into the SGC until they find a suitable planet to move to.

A rich industrialist has evidence to prove that there is alien life on other planets and gives the governments of the world 24 hours to reveal the truth or he's revealing it. The Air Force must decide how to handle the situation.

Teal'c moves into an apartment off-base where he becomes involved in a neighbor's problems. Meanwhile, Carter's boyfriend, Peter Shanahan, proposes and Carter tries to decide. Teal'c is then charged for murder and kidnapping and Daniel disappears while trying to prove Teal'c innocent.

The SGC experiment with a virtual reality chair from the Gamekeeper's world (season 2), but Teal'c becomes trapped in a virtual loop against an undefeatable batch of Anubis drones.

Daniel attempts to aid a battle-ravaged society when the team's appearance sparks a war.

Five days in the life of SGC as Jack assumes full command of the base and has to deal with a rapidly growing alien plant, the capture of SG-1 by Ba'al, arguing alien delegates, and a tricky traitorous System Lord.

A Russian Air Force Colonel comes to join SGC, as an alien creature shows up at the same time. The creature starts taking over members of the SGC. General O'Neill orders SGC to be locked down until the creature can be contained.

As the Replicators overwhelm the new Asgard homeworld, SG-1 works to revive Jack, create an Ancients weapon to stop the invaders, and tries to find the missing Sam, who is held captive by the humanform Replicator Fifth in a virtual reality.

While Sam and Teal'c go to the planet of the former human-form Replicators to contact the Asgard to cure Jack, Daniel and Dr. Weir must deal with Goa'uld System Lords who want the Ancients weapon the Tau'ri used to destroy Anubis.