During a trip to follow up on intelligence concerning a supposed Supergate, the Odyssey was attacked and ambushed by a group belonging to the Lucian Alliance members. It ended in tragedy when the Odyssey's commanding officer, Colonel Paul Emerson was murdered but thanks to the efforts of SG-1, the Odyssey and its crew were rescued and the Lucian Members Alliance were either captured or killed which also resulted in Emerson's murder being avenged.
Despite that success, it also marked the beginning of a war that pitted the Tau'ri against the Lucian Alliance, a war that continues to this day.
After the Battle of P3Y-229, there were political machinations at work in the upper echelons of the Lucian Alliance, and Netan, their leader, feared that one of his "Seconds" may be planning to overthrow him. His decision to commit ships to the battle against the Ori crusade proved to be disastrous. Furthermore, the Alliance was losing much territory as the Ori swept across the Milky Way galaxy. (SG1: "Camelot")
Netan sent one of his Seconds, Anateo, on a dangerous assignment to capture the Earth ship Odyssey, hoping that he would either die in the attempt or be disgraced. Meanwhile, the Tau'ri received some intelligence from the Jaffa that the Ori had constructed another Supergate elsewhere in the galaxy, and sent the Odyssey to investigate. (SG1: "Company of Thieves")
The Odyssey dropped out of hyperspace to investigate the reported second Ori Supergate. On board, Lt. Colonel Samantha Carter noted that the presence of Neutron star was powerful enough to disrupt Odyssey's systems. Immediately ambushed by three Ha'tak ships, Odyssey was forced into a minefield where the ship was extensively damaged. The ship's commanding officer, Colonel Paul Emerson, radioed Stargate Command and informed Major General Henry Landry of the ruse -- as Odyssey was boarded.
Carter awakened in the hold. Emerson reported they were towed out of the minefield. Members of the boarding party came for Carter, taking her and Emerson to Anateo -- part of the Lucian Alliance. He wanted Carter to disable the ship's subspace beacon, which was broadcasting their location. She refused, and Emerson ordered her not to cooperate. Solek, Anateo's lieutenant, shot Emerson in the heart and killed him.
Stalling on repairs, Carter was with Anateo when Dr. Daniel Jackson and Vala Mal Doran were brought on board. Anateo was upset that only part of SG-1 had been captured. As he had Jackson and Vala taken away, they told Carter it was part of a plan. She resumed her delaying tactics.
Carter instigated a plan to retake the Odyssey. Although Solek suggested presenting the Odyssey to Netan, Anateo believed that having the Odyssey and SG-1 would prove his leadership skills and allow him to unseat Netan. Carter continued her repairs and managed to open a door in the cargo hold, freeing Jackson and Vala. Teresh finally realized something is going on -- just before Jackson and Vala shoot him with a Zat'nik'tel.
When Anateo learned Jackson and Vala were missing, he threatened Carter. Before he could kill her, Vala accessed the ship's transporter system and beamed him into space, killing him. Afterwards, the crew retook the ship with no problems, capturing 14 Alliance soldiers, but Solek's fate is unknown as Vala was forced to beam him out too. A search of the ship failed to yield him so he most likely was beamed into space as well. The freed crew immediately started repairs as Odyssey had no working shields, no weapons, no communications, and no hyperdrive with focus being put on the hyperdrive as escape was the priority.
Jackson was in command of the bridge as Carter and Vala worked on the hyperdrive. Major Kevin Marks reported two Ha'taks had dropped out of hyperspace. Carter told Jackson to stall and Jackson took command of the ship.
Netan demanded that the Odyssey and its crew surrender and Jackson agreed, but suggested boarding would be difficult due to the ship's extensive damage, using it to stall for more time.
Onboard Tenat's Ha'tak, Lt. Colonel Cameron Mitchell was posing as Netan using a Tok'ra Reol chemical. As Tenat saw Mitchell as Netan, Mitchell ordered him to fire on Netan's Ha'tak. Teal'c hailed Odyssey, asking for transport and he and Mitchell were beamed aboard Odyssey as Tenat realized he had been duped. Netan then destroyed Tenat's Ha'tak.
Meanwhile on the Odyssey, Vala jammed a crystal into the array, which then lit up. With the ship's hyperdrive restored, Odyssey escaped into hyperspace before Netan could react. (SG1: "Company of Thieves")