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The Wraith civil war was the name given to a conflict that raged among the Wraith Hive ships after the Battle of Atlantis in 2005 when the race believed that the Ancient city of Atlantis was destroyed and, thus, their only hope to find a rich new feeding ground was over. (SGA: "The Siege, Part 3")
With the Human population of the Pegasus galaxy having yet to sufficiently repopulate since the last great culling 150 years earlier, the numerous Wraith Hives engaged in active conflict with one another to secure what precious few habitable Human worlds of the Pegasus galaxy were available. (SGA: "The Lost Boys", "The Hive", "Allies")
It is unknown as yet how the war with the Asurans has affected this conflict. The Wraith have been known to unite against common enemies, but as the Asurans have begun targeting humans and hoping to eliminate their food supply, this may exacerbate the already volatile situation. (SGA: "Lifeline", "The Seer")
Todd's faction in the war came into conflict with another faction who decided to use one of his feeding grounds. A Hive ship under Teyla Emmagan's command arrived and she ordered the enemy hive destroyed and a Wraith Dart attack launched in order to cause as many Wraith deaths as possible. In the battle that followed many of her Darts were destroyed and her Hive ship lost some of its weapons and was losing the battle until a Puddle Jumper flown by Lt. Colonel John Sheppard launched Drone weapons into the bottom of the enemy Hive causing a lot of damage. Teyla's Hive ship destroyed the enemy Hive easily after that scoring a victory for Todd's faction. (SGA: "The Queen")
Later, a Hive ship was enhanced by a Zero Point Module by the Wraith underling at the orders of Todd, resulting in the Super-hive. However, the Wraith underling later betrayed Todd and seized the Hive for himself. To stop the Wraith underling, Todd turned to the Atlantis expedition for help. The Hive ship was ultimately destroyed over Earth by a Nuclear warhead smuggled on board by Sheppard. Todd remains a prisoner on Atlantis, leaving command of his alliance to fall to Bonewhite. (SGA: "Enemy at the Gate")
Over time, a new Hive Queen known as Death came into power over the Wraith factions with her uniting a great many of them in the absences of Atlantis and the Atlantis expedition. She also later kidnapped the Chief Science Officer of the expedition, Dr. Rodney McKay and had him converted into a Wraith named "Quicksilver" with McKay/Quicksilver becoming one of Death's loyal followers. (SGA, "The Lost")
McKay was eventually rescued and returned to human form while Guide began gathering a new following to oppose Queen Death with the help of Teyla disguised as his queen, Steelflower. After learning that Atlantis had found Hyperion's weapon, Queen Death launched an all-out attack on Atlantis. Atlantis, the George Hammond, the Pride of the Genii and eventually a small Wraith fleet led by Guide defended Atlantis and battled Queen Death. Queen Death was killed by Teyla and her forces suffered heavy losses during the battle. Following Queen Death's end, her remaining forces surrendered to Queen Alabaster, Guide's daughter. (SGA: "Inheritors")