The Abydos Mission was an Federation operation led by Colonel Jack O'Neill, and his team in 2359 and first official mission to the planet Abydos. It eventually resulted in the death of the Supreme Goa'uld System Lord, Ra, while freeing the Abydonians from Ra's control. It also marked the beginning of the Federation-Goa'uld War.
After years of unsuccessful tests, Dr. Catherine Langford, Professor Langford's daughter hired Dr. Daniel Jackson to decipher the symbols on the Cartouche. Over the course of the next two weeks, Jackson puzzled over the mysterious seven symbols in the center of the cartouche. Due to a chance incident, he discovered that these seven symbols were not words to be translated, but in fact star constellations. When explaining his findings to Major General W. O. West, the leader of the project, Jackson stated that the cartouche charts a course to a point in deep space with seven symbols—six for the destination and one for the point of origin. West decided to show Jackson the artifact discovered in 1928—the Stargate itself. After Jackson quickly discovered which symbol on the gate is the point of origin, the gate was activated, creating a wormhole between it and another gate "on the other side of the known universe." An initial probe was sent through the gate, revealing the planet on the other side can support human life. Once findings came back as positive, a team led by Colonel Jack O'Neill traveled to the planet Abydos to explore it. O'Neill, Jackson, Lieutenant Charles Kawalsky and Lieutenant Brown visited the Abydonian city Nagada.
Ra arrived in his ship and had his Horus Guards attack the team members still in the Abydos pyramid. In the skirmish that followed, Lieutenant Porro and Lieutenant Reilly were killed while both Lieutenant Louis Ferretti and Lieutenant Freeman were captured. When Colonel Jack O'Neill, Dr. Daniel Jackson, Lieutenant Charles Kawalsky and Lieutenant Brown returned to the pyramid, they find Ra's ship overlooking it and armed themselves before entering. Brown was killed and Kawalsky was captured while O'Neill tries to arm a Mark III photon warhead that he had brought along in case of threats, but found that the bomb was gone. Anubis and Horus arrived down via the Transportation rings and O'Neill and Jackson were forced to surrender or die. They surrendered and were taken aboard the ship where O'Neill managed to get a Staff weapon and killed one of the Horus guards, but Jackson was killed and Ra was shielded by the children that followed him while O'Neill was beaten down when he hesitates to fire.
After Ra resurrected Jackson in his Sarcophagus, essentially bringing Daniel back to life, Ra forced Daniel to execute his friends publicly, but a group of young Abydonians, led by Skaara and Sha're, having learned their history from Jackson, rebelled and created a distraction (using the weapons and equipment from O'Neill's camp), allowing Jackson to shoot at Ra and escaped with the team, though a few Abydonians and Freeman were killed. The next day, the team and the rebels infiltrated the miners and O'Neill killed Horus. Jackson exposed Horus' face to the Abydonians to show them that their gods were just regular men. The team then joined the caravan that delivered a tribute of Naquadah to Ra. Jackson, O'Neill and Sha're went inside the pyramid with a few of the rebels while Kawalsky and Ferretti along with the rest of the rebels waited outside. O'Neill was revealed and a firefight was triggered that left two of the three Horus guards dead and all but himself, Jackson and Sha're killed.
The last Horus guard closed the door and shoots a blast that knocked everyone outside (charging the temple) off their feet before O'Neill killed him with a staff weapon. Ra dispatched two Death Gliders to deal with the group outside who created a bunker from the caravan carts, but the group ran out of ammo quickly with several of the group, including Nabeh being killed. In the pyramid, O'Neill discovered the bomb and armed it, but before he could do anything else, Sha're was killed by a Horus guard that Jackson later killed. Desperate, Jackson used the opportunity when Anubis ringed down to send the bomb to Earth to ring to Ra's ship and also used his sarcophagus to resurrect Sha're while O'Neill fought Anubis while also attempting to disarm the bomb.
Outside, the group was forced to surrender to the Horus guards who had landed, but the rest of the Abydonians, led by Kasuf, rose up in rebellion against them and defeated the guards. Ra found Jackson on the rings trying to return to the pyramid and started torturing Jackson with his Kara kesh, the effect slowly killing Jackson. O'Neill managed to get the better of Anubis and positioning him under the rings, activated them, decapitating Anubis which resulted in Anubis's death. On the ship, Jackson managed to break free as the rings activated and he and Sha're escaped as Anubis' head traveled to the ship.
Seeing that they won, O'Neill tried to deactivate the bomb, but was unable to as Ra rigged it. Having lost, Ra prepared to leave Abydos in his ship. With less than a minute left and no way to disarm the bomb, Jackson and O'Neill came up with the idea to send the bomb to Ra's ship. They ringed the bomb on board and Ra could only watch in horror as the bomb arrived. Seconds later, it exploded, destroying the ship and killing him.
After dialing the Stargate back to Earth, Dr. Daniel Jackson chose to stay on Abydos and marry Sha're while Colonel Jack O'Neill, Lieutenant Charles Kawalsky and Lieutenant Louis Ferretti returned to Earth. Following their return, the Stargate Program was shut down and the Stargate transferred to Cheyenne Mountain with the new Stargate Command being left vacant as well. However, the death of Supreme System Lord Ra caused upheaval in the Goa'uld Empire and alerted the System Lords to the presence of Earth, eventually triggering the start of the Federation-Goa'uld War, a war that would rage in the galaxy for 23 years.
- In an alternate reality visited by Daniel Jackson in 2361, Jack O'Neill likewise led the first mission through the Stargate to Abydos with the intention of detonating a photon torpedo. However, the Daniel Jackson of that reality was not involved in the mission due to the fact that he had turned down the offer to join the Stargate Program. Like his counterpart in our reality, Jack was willing to commit suicide following the recent death of his son Charlie O'Neill. Ra was likewise killed during the mission, though it is unclear if his death occurred under the same circumstances as in our reality. Ra's death indicated to the Goa'uld that the Humans were a significant threat to them, resulting in Apophis' devastating attack on Earth in 2361.
- In another alternate reality, it was Doctor Samantha Carter rather than Daniel Jackson who discovered how to operate the Stargate. Although it is not specifically stated, it can be assumed that, in this reality, the first mission through the Stargate was likewise to Abydos.