Upon receiving intelligence that the Tau'ri were in possession of Ancient knowledge and technology, the goa'uld system lord Anubis launched a massive assault force to Earth consisting of the full force of his fleet, in clear violation of the Protected Planets Treaty. As a result of the engagement, Anubis' fleet was completely destroyed, resulting in a tremendous victory for the Tau'ri and vastly shifting the balance of power among the remaining System Lords.
Having learned of the existence of one of the Ancient's Repository of knowledge on P3X-439, SG-1 went there to acquire the information, hoping to locate the Lost City of the Ancients. When they learned the Goa'uld System Lord Anubis was on his way, Colonel Jack O'Neill decided to destroy the device. Dr. Daniel Jackson tried to have knowledge downloaded into his brain, but O'Neill stopped him, having it downloaded into his instead, as well as destroying the device. Anubis, upon learning this, decided to attack Earth. SG-1 returned to Earth, only to discover that Major General George S. Hammond had been relieved by the newly inaugurated President Henry Hayes, at the urging of Vice President Robert Kinsey.
Hammond's replacement, Dr. Elizabeth Weir, was swayed to allow SG-1 to take a Tel'tak to travel to Proclarush Taonas. There, O'Neill activated an Ancient star map, bringing up a hologram of Earth and saying two words in Ancient: Terra Atlantus. The Lost City of the Ancients is the Lost City of Atlantis, and it was on Earth. Daniel and Major Samantha Carter were dumbfounded to have traveled here but O'Neill also revealed that he needed a Zero Point Module. (SG1: "Inauguration", "Lost City, Part 1", "Lost City, Part 2")
Battle above the iceEdit
Anubis sent three Ha'taks that destroyed the Nimitz battle group. After that, he appeared in the Oval Office, using Asgard hologram technology, and demanded Earth surrender to its "god", Anubis. In response to President Henry Hayes refusing to be intimidated, Anubis brought another thirty plus motherships with him including one of his super motherships.
Colonel Jack O'Neill, having modified the engines of the Tel'tak with the help of Major Samantha Carter to get them to Earth in time, also modified the Transportation rings to burn through the ice of Antarctica, which is where Atlantis was supposed to be. They relayed their information to Earth, asking for help to succeed. While Vice President Robert Kinsey tried to relieve Dr. Elizabeth Weir of command, Hayes "accepted" Kinsey's resignation, and sent the Prometheus under the control of Major General George S. Hammond to assist. The fleet of 20 F-302 fighter-interceptors, all that had been built, lead by Major Cameron Mitchell, was able to arrive quick enough to provide cover fire, while the Prometheus acted as a shield against potential orbital bombardment. Mitchell himself shot down an Al'kesh trying to attack the Tel'tak, but was soon shot down himself, Mitchell being gravely injured.
Finally, when the F-302s had expended all their ordinance, Anubis' mothership was in place to attack the Tau'ri. Hoping to buy them time, Hammond ordered the Prometheus to ram the mothership. SG-1, meanwhile, ringed into the Antarctic outpost. Anubis' sensors had also located the outpost, and he sent a hologram of himself there to taunt them. Kull warriors then ringed down to secure the base. As SG-1 covered him, O'Neill replaced the depleted Zero Point Module in the platform with the ZPM taken from Proclarush.
The power of the AncientsEdit
In the end, Colonel Jack O'Neill was able to access the Antarctic outpost's defensive system via the Control chair by using his ATA gene. On Jack's mental command, thousands of Drone weapons were launched, some of which enveloped a Kull warrior. Flying through the hole O'Neill had burned through, the drones proceeded to orbit. They completely bypassed the Prometheus and went straight for Anubis' mothership, then quickly spread to the rest of the Goa'uld fleet, easily piercing their shields. Prometheus was able to break off course in time to avoid ramming Anubis' mothership. As Her'ak declared the ineffectiveness of the shields, a set of drones targeted the Pel'tak. Anubis' mothership was then destroyed, presumably taking the System Lord with it.
Unfortunately, the strain of controlling a powerful weapons system put a huge strain on Jack's already taxed body, essentially resulting in him being left near death. As such, Jack was placed into an Ancient stasis pod. Major Samantha Carter was convinced that they could find a way to save him in the city, but Daniel had already concluded that the structure was not Atlantis itself, simply an outpost of some kind. Unable to help, SG-1 merely stared at O'Neill, frozen in time. (SG1: "Lost City, Part 2")
Sometime after being placed in stasis, O'Neill was revived thanks to the efforts of the Asgard and returned to normal. Jack also created a Replicator disruptor that would destroy the Replicators. Following his return to Stargate Command, Jack was promoted to the rank of Brigadier General and also became the new commander of Stargate Command, replacing George S. Hammond who was promoted to Lt. General and appointed to head the Office of Homeworld Security, which would oversee the SGC, Atlantis military contingent, and the BC-303 and 304. (SG1: "New Order, Part 1", "New Order, Part 2")
Now the official commander of the SGC, O'Neill stepped down from his position as the team leader of SG-1, a role he'd held for the last seven years, and promoted his former second-in-command, Major Samantha Carter to the rank of Lt. Colonel. This also resulted in Sam becoming the new commanding officer for SG-1. SG-1 itself remained a three-man team for the duration of Jack's term as head of the SGC.
Dr. Elizabeth Weir, Jack O'Neill's predecessor at the SGC, was appointed head of the research team that studied the Antarctic outpost. After learning that Atlantis had headed for the Pegasus galaxy, she petitioned O'Neill to lead an expedition to the Lost City. Among the members of the Expedition were Lieutenant Aiden Ford, Major John Sheppard and Dr. Meredith Rodney McKay. O'Neill agreed, and the Atlantis expedition was launched using the Zero Point Module found which ultimately depleted it, resulting in the Expedition being left stranded in Atlantis and in the Pegasus Galaxy. It would be over a year before they would be able to re-establish a new and permanent connection to Earth, enabling them to stay in contact with both the SGC and Earth itself. (SGA: "Rising")
During the battle, Colson Industries satellites captured images of Anubis' fleet exiting hyperspace in orbit of Earth and the Prometheus under attack in Antarctica. The company's CEO Alec Colson attempted to go public with this information five months later but his efforts were thwarted by the Trust. (SG1: "Covenant")
Though Anubis' semi-ascended nature allowed him to survive, and briefly take hosts by moving from people stationed in the SGC, he was presumed dead. Having been the dominant force in the Goa'uld Empire for two years, his disappearance was almost as chaotic as the death of Ra had been. To avoid the war that followed the deaths of Apophis and Cronus, the System Lords divided his territories, but Ba'al was able to learn the location of the Kull warriors, and took control of them. Ba'al eventually conquered the rest of the System Lords, though he was defeated in the Battle of Dakara. (SG1: "New Order, Part 1", "New Order, Part 2", "Lockdown", "Reckoning, Part 2")
Major Cameron Mitchell, who had participated in the F-302 battle against Anubis's armies, was left badly injured when the plane he was in crashed. After being hospitalized, Mitchell, who had lost the ability to walk, regained it with physical therapy. During his time in the hospital, Mitchell also read the reports concerning SG-1 with Mitchell himself being promoted to Lt. Colonel. Mitchell later arrived at Stargate Command with the hope of joining SG-1, only to learn from his new C.O. Major General Henry Landry that all the original members of SG-1 had moved on and were all working on different projects. With the Ori becoming an increasingly dangerous threat, Mitchell was eventually able to reunite the members and as such, continued to lead SG-1. (SG1: "Avalon, Part 1", "Ex Deus Machina")
- In an alternate reality which Lt. Colonel Samantha Carter was accidentally transported to in January 2007, the existence of the Stargate Program was eventually revealed to the general public and martial law was declared in the United States of America during Anubis's attack on Earth in 2004 which later triggered riots all over the United States. Although SG-1 found the Control chair from the Antarctic outpost, they could not power it sufficiently to use it against Anubis's fleet and the attack continued. The fate of the Colonel Jack O'Neill of this reality was never made clear although it is possible that he was never removed from the Ancient stasis pod in the Antarctic outpost. It is unknown what happened to Anubis as he is not referred to afterwards. It is likely that either they managed to defeat him or that the Ori dealt with him. The Cameron Mitchell of this reality likewise crashed his F-302 fighter-interceptor but unlike the main reality where Mitchell made a full recovery, was promoted to the rank of Lieutenant Colonel and eventually became leader of SG-1, the Mitchell of that reality never made a full recovery, remaining permanently paralyzed as well as confined to a wheelchair. At first, Mitchell was treated as a hero, even participating in a number of PR events but after Mitchell criticized the program for its martial law, he stopped receiving treatment and presumably left both the military and the Stargate Program for good as a result with the Mitchell of that reality becoming an angry, bitter cripple furious over his treatment who had also taken up smoking as well.(SG1: "The Road Not Taken")