At some point in the Lantean-Wraith war, the Avenger suffered heavy damage in battle with enough hull breaches to force a crash on an uninhabited planet. The crew either suffered no casualties or the survivors took them with them when they left through the planet's Stargate as no bodies were found on the ship.
At some point, 10,000 years later, the Genii discovered the wreckage of the Avenger and set out to repair the ship as their own. Repair teams led by Dahlia Radim were able to repair sublight engines and hyperdrive over the course of a year, but lacked the ATA gene and so could not get the ship's power or systems online. They also patched some of the hull breaches and closed the bulkheads to deal with others.
In 2009, after Doctor Rodney McKay is kidnapped by the Wraith, Lt. Colonel John Sheppard approaches Ladon Radim, Chief of the Genii for help finding him using the Genii's extensive intelligence network. Ladon offers a deal in which he will search for McKay if the Atlantis expedition aids the Genii in moving the Avenger to their homeworld, believing the repairs done to the ship have made it spaceworthy enough to make the trip to the Genii homeworld. Sheppard agrees to this deal, but due to a Wraith attack, the team loses their Puddle Jumper and Doctor Carson Beckett is seriously injured by reptiles while making their way to the ship.
Once aboard the Avenger, Sheppard determines that while they have sublight engines and hyperdrive, they don't have shields, weapons control or long-range communications and the structural integrity is "lousy" with many of the bulkheads unlikely to hold up under vacuum. Rather than risk a seventeen hour trip to the Genii homeworld, Sheppard chooses to take the ship to Atlantis which is six hours away where rescue will be on hand if the ship cannot be landed safely and further repairs can be done to make it more spaceworthy. During takeoff, during which the crew wears vacuum suits for safety, the ship suffers decompression in two compartments aft of engineering which Dahlia is able to seal off. Upon reaching space, one of the potable water and water reclamation tanks suffers a decompression and vents to space as well, but the ship suffers no more decompressions and after an attempt by Dahlia to hijack the ship, Sheppard is successfully able to take the Avenger to hyperspace.
Arriving at Atlantis, Sheppard has the city prepare a rescue Puddle Jumper in case he needs to ditch the Avenger in the ocean, but he is able to make a safe landing on the North Pier of Atlantis. Once at Atlantis, a team led by Doctors Radek Zelenka and Miko Kusanagi work on repairing the ship enough to get it to the Genii homeworld with Ladon demanding the ship be sent within a day after learning of the situation. The repair teams are eventually able to close the hull breaches, particularly two nasty ones aft of engineering.
After the Avenger is spaceworthy once more, Sheppard flies the ship to the Genii homeworld accompanied by Kusanagi, a team of Marines and Dahlia. The ship is also escorted by the George Hammond in case of troubles. Despite some minor power fluctuations, the Avenger is able to make the thirteen hour trip to the Genii homeworld without incident and Sheppard lands the ship in a camouflaged field. (SGA: "The Lost")
When news comes of Queen Death's impending attack on Atlantis, Ladon offers Atlantis use of the repaired Avenger, now renamed the Pride of the Genii in defending Atlantis in exchange for giving his people the ATA gene therapy. Though reluctant to give the Genii the gene therapy, Richard Woolsey agrees and the Pride of the Genii, piloted by Major Evan Lorne and with a crew containing Ladon himself, fights in the battle alongside a Wraith fleet loyal to Guide, the George Hammond and Atlantis itself. During the battle, the Pride of the Genii takes on several F-302s unable to return to the George Hammond and sends a Genii boarding party to Queen Death's own hive ship to aid another boarding party led by Teyla Emmagan from a captured Wraith cruiser. (SGA: "Inheritors")