After Atlantis left to defend Earth from the super-hive, Queen Death rose to power amongst the Wraith and began uniting the Wraith under her control and decimating worlds after feeding on them. Upon their return to the Pegasus Galaxy, the Atlantis expedition learned of Queen Death's rise to power and began opposing her. At the suggestion of her chief scientist Dust, Queen Death captured Doctor Rodney McKay and transformed him into a Wraith named Quicksilver. As Quicksilver, McKay led a raid that stole Atlantis' ZPM, leaving the city defenseless. While believing he is a Wraith, Quicksilver also gives the Wraith energy shields that they incorporated into their ships. Wishing to launch an attack on Atlantis, Queen Death is convinced send a bomb through the Stargate and a small force by ship to attack from space and test Atlantis' defenses as while she has a powerful alliance, she lacks the strength to launch an all-out attack and win. The Wraith send a hive ship and the Wraith cruiser Eternal to probe Atlantis' defenses while their attack by Stargate fails to penetrate Atlantis' new mechanical iris once again.
Three days after the failed Stargate attack, first the Eternal and then the hive ship are detected dropping out of hyperspace in Atlantis' solar system inside the orbit of the last planet, four to five hours travel from Atlantis. Upon arrival, the two Wraith ships begin scanning at very low power, detected by Doctor Radek Zelenka, but neither begin approaching the city yet. Zelenka, Lt. Colonel John Sheppard and Colonels Steven Caldwell and Samantha Carter discuss their options, knowing that they can't let the Wraith ships detect that Atlantis has no shield but also reluctant to launch the Daedalus and George Hammond against a hive ship and a cruiser. Zelenka also states that while Atlantis has a new ZPM with a little power, it is very minimal and the shield could only be raised for possibly a minute before it collapses again and they can only fire a few drones at most. As Sheppard, Carter and Caldwell discuss options for possibly attacking the Wraith ships, the Wraith begin moving in-system towards Atlantis, ending the debate. Checking Atlantis' long-range sensors, Carter and Caldwell find a spot to intercept the Wraith ships where they will have a good chance of stopping them before their Wraith Darts can reach the city. With the ships seven hours out, the Daedalus and George Hammond are prepared for launch while Sheppard situates himself in Atlantis' Control Chair and security teams are dispatched throughout the city in case the Wraith beam in any forces during the battle. (SGA, "Legacy: Homecoming", "The Lost", "Allegiance")
The hive and it's escort drop out of hyperspace, and start scanning for Atlantis. They close on the planet to get a better look, but they are intercepted by the two battlecruisers. At this point the Tau'ri learn that the hive is using an energy shield, something they have never previously encountered on a Wraith ship. A long fight ensues, with the Hammond keeping the hive busy while the Daedalus takes out the cruiser. Although the cruiser is disabled the Daedalus takes damage to their engines, redering them unmovable. The Hammond continues to fight, keeping the inert cruiser between it and the hive. Colonel Carter prepares to crash the ship into the hive in a last desperate measure, after beaming off her crew, but then the beams go offline and she prepares for the kamikaze run. As Carter performs her suicide run, the Daedalus rejoins the fight, distracting the hive ship. Seeing her chance as the hive ship turns its damaged stern towards the Hammond, Carter diverts all power to the rail guns and fired. The rail guns were able to fire five shots before the Hammond lost all power. The shots impacted the hive ship's damaged stern, destroying the ship. While Carter would've died on the powerless Hammond, the Daedalus was able to save her by beaming her aboard. (SGA: "Allegiance")
- This is one of the first times that human ships have been able to take down a hive without nuclear warheads, Ancient weapons or such.
- Carter's attempt to perform a suicide run with the George Hammond is similar to what she did in an alternate timeline with the Phoenix, the Hammond's counterpart in that timeline. Unlike there, she and her ship survived the battle.