New Order, Part 2

Plot
Thor is informed by Penegal of the Asgard Council that several Replicator blocks rained down on Orilla and started to infest Asgard systems needed to save the minds and cloned bodies of the Asgard. And the Asgard aren't able to evacuate their new home. In the meantime the Prometheus waits in Earth orbit on the Goa'uld ship but it turns out that the ship is in fact Thor's ship and they are greeted by Teal'c. At SGC Daniel informs the System Lords that their ship was destroyed by Ba'al and he is suddenly beamed aboard Thor's ship, the Daniel Jackson. After he is greeted Thor beams up O'Neill, whose Ancient-knowledge would be the key to destroy the Replicators.

Meanwhile Carter wakes up in a bed and it turns out that she is in a large farmhouse in Montana. She is greeted by Pete Shanahan but doesn't believe that this all is real. However Pete tells her that she left SGC a year ago due to mental stress and after some time she finally agrees to eat something. After a meal she says that she still don't believe that this is real which makes Pete angry. Finally Pete transforms into Fifth who tells her that he loves her. She however tells him that she can't love him back so he threatens to make her very unhappy.

On Thor's ship he connects O'Neill's mind with the computer of his ship with a stasis pod sustaining his life and the computer translating Ancient. Finally O'Neill talks to them through the ship' communication and lets the lights flash since he has control over the ship. He then shows himself as a hologram and starts to work on something to fight the Replicators. After some time an alarm sounds because the Ancient knowledge must be erased and O'Neill is barely able to finish his work before he is woken up. When he gets up he still feels dizzy and doesn't remember what happened. Meanwhile Thor materializes the device which O'Neill created but he doesn't know what it is. Suddenly they are contacted by Penegal who informs them that the Replicators on Orilla seem to be controlled by a human-form Replicator and so SG-1 hopes that Sam survived but it turns out that the Asgard found no life signs of her. Then the communication is disrupted.

At SGC Weir visits Yu's First Prime Oshu who asks her to let them go to fight against Ba'al since he commands the full force of Anubis' fleets with which he would control the galaxy. Later she visits Camulus who wants to request asylum since his forces were destroyed. Finally the System Lords are allowed to leave but Amaterasu tells Weir to tell Camulus that he will be forever branded a traitor and a coward.

While Thor still does researches on the Ancient device he is contacted by Aegir, commander of the Valhalla, who tells him that they found the remains of a human-form Replicator in space, which Thor beams on board. He then tries to enter the Replicator communication network. Thanks to this they find out where Carter is but then the human-form Replicator wakes up, repairs itself, resists beaming and takes control of the ship. The three humans fire on him but to no avail until O'Neill uses the Ancient weapon – which turns out to be a disruptor – to destroy the Replicator. Thanks to this new information Thor will be able to generate a large version of the weapon to destroy all Replicators on Orilla.

In the meantime SG-1 beams down on the planet to rescue Carter. They are quickly attacked by Replicators which they start to destroy until Fifth appears, who threatens to kill Carter. O'Neill is then contacted by Thor but suddenly all the Replicators start to move in one direction. SG-1 tries to destroy as much of them as possible until they see a massive Replicator ship in the form of a large spider. Meanwhile Carter talks with Fifth, who tells her what is happening. She tries to talk some sense into him when suddenly the ship leaves. Afterwards Thor activates the massive disruptor which destroys all remaining Replicators on the planet. He then detects another life sign in the proximity of the three humans and it turns out to be Carter. So SG-1 is finally reunited.

Some times later O'Neill visits Weir who tells him that she will supervise the Ancient outpost. She also tell him that General Hammond will be the new director of the new unofficial "Department for Homeworld Security" and that the new commander of SGC will be Brigadier General Jack O'Neill since the Pentagon believes he's perfect for the job. Although he is happy about the promotion he doesn't like to be in charge of something, which he also points out during his meeting with SG-1. However they assure him that he is the best for this position but that there are also new challenges for all of them.

In the end a large meeting is held in the gate room during which Weir says goodbye and presents the people their new commander. O'Neill then holds a speech and as his first command he promotes Major Carter to Lieutenant Colonel.

On the Replicator ship Fifth is very happy so see that the new human-form Replicator is completed, which has the form of Carter.