The Second Battle of Atlantis was the conclusion of the war against Queen Death.
Following the Atlantis expedition's discovery of Hyperion’s weapon, Queen Death’s advisor the Old One, formerly known as Ashes; one of the original Wraith created, presses her to attack Atlantis before the weapon can be used. (SGA, “Secrets”)
Following the discovery of Hyperion’s weapon, Richard Woolsey had Colonel Sheppard hide the weapon while he took measures to prevent the IOA discovering the weapon existed. Rodney McKay using his residual telepathy found the location and decided to move it to prevent the location being taken from Sheppard by the Wraith Queen Alabaster who they’d found with the weapon. Meanwhile, Colonel Carter was able to inform General O’Neill of the weapon bringing him to Atlantis where Guide set the terms that any further assistance from his alliance would only happen once the weapon had been destroyed.
Meanwhile, a Genii spy posing as a Wraith worshiper received intelligence that Queen Death was making an attack on Atlantis and headed back to the Genii homeworld to warn Ladon Radim. Once received, Radim and his agent headed to Atlantis in order to pass on the intelligence and to offer the Pride of the Genii’s assistance in return of the ATA Gene Therapy.
When the agent began to go through withdrawal, Woolsey allowed Alabaster to partially feed to restore him and confirm the intelligence whilst McKay and Zelenka used the Deep Space Sensors to detect the presence of Death’s fleet.
Upon the discovery that the weapon was gone, McKay is placed in the brig under suspicion, he reveals where he placed the weapon not realizing that Ronon had found and removed the weapon himself and failed to hand it to Sheppard. Believing that the McKay may still be working for Queen Death they keep him locked up.
Sheppard and O’Neill plan to use the City as a mobile weapons platform and take on the Wraith fleet in space alongside the Hammond and the Pride of the Genii, as Guide refuses to fight without seeing the weapons destruction.
In order to complete preflight, in time they are forced to let the unjustly imprisoned McKay out so as to make the City ready to fly.
Just before launch, McKay is once more placed back in the brig.
Meanwhile, Alabaster who’d taken command of Guide’s alliance brought his ships to Atlantis’ solar system following the discovery of a spy on board Guide’s ship.
Once the Wraith arrived, the Pride of the Genii and the George Hammond performed a hyperspace microjump to engage with Death’s fleet, while Atlantis took flight and remained in a support position, meanwhile Guide true to his word kept his fleet distant and refused to engage.
During the engagement the Pride and the Hammond became blocked in and where being overwhelmed forcing Atlantis to take an active part in the engagement, at the same time McKay escaped his cell to try to locate Hyperion’s weapon. During the engagement one of the Wraith cruisers was damaged and seemed to be using vented atmosphere to propel it's self closer to Atlantis having been filled with explosives.
Sheppard then discovered Ronon with Hyperion’s weapon and talked him down, taking the weapon and intending to fly it into the sun to gain Guide’s assistance however Rodney stuns him and takes his place, flying under cloak towards the sun.
In the midst of the battle Waterlight’s hive ship arrives and begins to attack Death’s somewhat evening the odds, at the same time Teyla leads a team including Dr Zelenka to the damaged cruiser to disarm the explosives.
while traveling through the battle McKay’s jumper is damaged forcing him to kamikaze the sun to destroy the weapon, he decloaks and informs the surrounding fleets of his intention, both Colonels Crater and Sheppard try to stop him however he closes the channel and is beyond the Hammond’s range. After cutting the signal he is joined by an Ascended Dr Elizabeth Weir who uses her powers to transport him to the Hammond’s infirmary.
Guide’s forces move to assist turning the tables, sending his chief clever man Ember to the cruiser to assist disarming while he gives Atlantis his the identification codes for his wave of darts. Once the explosives are disarmed Teyla and Ember use the cruiser to board Death’s hive ship, joining with Waterlight Teyla helps to reach Death’s chambers where she engages with a telepathic contest, however Death is victorious forcing Teyla to reveal herself as Queen Steelflower before defeating her. Teyla offers Death mercy which Death refuses leaving Teyla no choice but to kill Death ending the battle. (SGA, “Inheritors”)
In the aftermath of the battle Teyla, Alabaster and Waterlight stand in judgement of Ashes, the two Wraith Queens offer Teyla the right to punish Ashes however Teyla refuses saying that enough blood has been spilled in the name of revenge she leaves Ashes to her sisters.
A treaty is reached with the Wraith awarding them half of the Galaxy and a retrovirus that allows humans to survive feeding.
Meanwhile, McKay begins to push for the team to search for Elizabeth Weir knowing that just like Daniel Jackson, Orlin and Morgan le Fay before her she will be most likely punished by the Ancients for saving Rodney’s life.
- The Ancient warship and the Daedalus-class battlecruiser depicted here have tractor beams used in assisted landing/retrieval of small objects into the landing bay. This feature was never mentioned or depicted on screen or in other sources.
- Although the Others punished Elizabeth for saving McKay’s life, they didn't stop her from saving him. This is in contrast to when the Others prevented Daniel from attacking Anubis in Threads or when they pulled Morgan out before she could tell Daniel the Sangraal’s location in The Pegasus Project.