In the Milky Way galaxy an Asgard ancestor is discovered so a lab is set up on Adara II, a protected planet for Heimdall to study the ancestor in order to try to learn a way to fix the Asgard cloning problem. Anubis learns of this and dispatches Osiris with two upgraded Ha'taks to capture the lab. Learning of this, the Asgard send Supreme Commander Thor with a Bilskirnir-class ship to defend the lab. This is believed to be enough to enforce the treaty as the Goa'uld ships in the past haven't been able to match a single Asgard vessel and the rest of the Asgard fleet is busy engaging the Replicators.
When Osiris refuses to withdraw, Thor is forced to open fire, but Osiris' ship's shields absorb the attack. With its upgraded Staff cannons and presumably the help of the other mothership, Osiris' ship destroys Thor's ship. Thor escapes, but is captured by Osiris.
With no ship able to reach Adara II and rescue Heimdall and his research, Freyr approaches the Tau'ri for help with doing the job as they have a Tel'tak. Colonel Jack O'Neill agrees to the mission and SG-1 travels to Adara II. There they land on the surface after cloaking and are beamed to the facility by Heimdall. There Heimdall explains that Thor survived and was captured and is able to project a hologram of O'Neill to Thor after Osiris leaves. Thor tells O'Neill to take Heimdall and his research and leave as Anubis himself is coming to get the secrets of Asgard technology. The team comes up with a plan: when Anubis arrives, O'Neill and Teal'c will use the Tel'tak's Transportation rings to board the Ha'tak at the same time and then take out the shield generator so Heimdall can beam them out. The two successfully ring onto the ship into an unoccupied ring room, but are detected. Jaffa are sent to deal with them, but thanks to a holographic trick by Major Samantha Carter, they manage to take out some of the Jaffa and continue on their way. At the same time, Anubis uses a mind probe to link Thor's mind to the ship's computer and learn his secrets. Needing to stop O'Neill and Teal'c, Osiris has the lower decks of the ship sealed off and coolant from the hyperdrive sent into the vent system. While this causes the death of many Jaffa in the engine room, it also knocks out O'Neill and Teal'c and they are captured.
After waking up, O'Neill and Teal'c are contacted by Thor who is able to use his connection to the ship's computer to free them from their cell. Carter, after helping Heimdall connect the Stasis pod with the Asgard ancestor to the Tel'tak's systems, returns to the lab to guide them as a hologram to a control relay to pull the Control crystals which will give Heimdall a few seconds to beam the two and Thor out while the crew switch to back-ups. At the same time, a battle with Lord Yu goes badly so Osiris sends the other two Ha'taks to help while a Death Glider locates the lab. Osiris and some of her Jaffa head there while O'Neill and Teal'c are guided to the relay by Carter. Before she can tell them which crystal to pull, they are attacked by Jaffa and she is shot with a Zat'nik'tel by Osiris and her men. Osiris starts to torture Carter with her Kara kesh for information on Dr. Daniel Jackson while O'Neill, unable to decide which crystal to remove, shoots them all with a Staff weapon. With the shields down, Heimdall is able to beam O'Neill, Teal'c and Thor out and Carter from the lab.
Having gotten what they needed, Teal'c quickly flies the Tel'tak out of the atmosphere while Thor warns them that he should be left behind as he is still connected to the Ha'tak's computers and thus can be tracked. The ship clears the atmosphere, but Anubis is able to detect the ship and opens fire before it can enter hyperspace and takes down its hyperdrive, cloak and shields. Anubis contacts the ship and demands surrender, but Heimdall wants them to blow themselves up rather than allow themselves to be captured. Luckily before they can do anything, Freyr arrives with three O'Neill-class ships and demands Anubis retreat or face the Asgard ships in battle. As the Asgard ships are superior to both Thor's ship and his own, Anubis retreats without a fight.
SG-1 successfully completes its mission and Heimdall and his research are saved. However, Thor goes into a coma as, unknown to anyone, his mind was downloaded into the Ha'tak's computer. Sometime later, Thor takes complete control of the ship and flies it to Earth where his mind is rescued and he is downloaded into a new body.