- "As you know, the Wraith are at war... I believe you refer to our enemy as 'Replicators.'"
The Pegasus Replicator War was a year-long conflict in the Pegasus Galaxy, largely pitting the infighting factions of the Wraith against the suddenly-active Asurans. Spurred by the Atlantis Expedition's decision to reactivate the Ancient machines' prime directive, that being to attack and destroy the Wraith, the war quickly grew to include every living thing in the galaxy, particularly the humans whom the Replicators targeted to deprive their enemy of a food source. While incredibly destructive on both sides, the war had the effect of forcing the Wraith to begin constructing new ships and cloning more soldiers, and would ultimately pave the way for the redevelopment of the long-forgotten superhives.
After the Ancients' failed attempt to destroy them, the Asurans managed to build their own city and fleet of ships utilizing Ancient technology.  At first, they followed their initial directive and attacked the Wraith; but the Wraith devised a means to deactivate this part of their programming. They were apparently no more able to destroy the Asurans than the Ancients were, however, and a team from the Atlantis Expedition, led by Doctors Elizabeth Weir and Rodney McKay, managed to reactivate the command. The Asurans soon launched a new attack against the Wraith. In the war's initial stages, the Asurans seemed to be doing quite well, with fighting on several fronts. The Wraith attempted once again to deactivate their attack command, then orchestrated the capture of Doctor McKay in order to help them, but had no success.
- "They realized we have a significant vulnerability: our food supply. They have begun to annihilate human worlds."
As the war progressed, the Wraith appeared to be having more success in battling the Asurans than during its initial stages.  Perhaps as a result, the Asurans began to adopt a new strategy — to eliminate the Wraith food supply by destroying the galaxy's human population. Tens of thousands of humans, accounting for the populations of entire worlds, had been killed in this way by the time the Atlantis Expedition learned of this development; as a result, the expedition entered into cooperation with a Wraith in order to deactivate the Asurans' attack command. 
Battle of AsurasEdit
- Main article: Battle of Asuras
The Daedalus, Apollo, and seven Travelers ships joined seven Wraith Hive Ships in an attack on the Asuran homeworld, which the Daedalus and the Apollo had forced the Asurans to retreat to. The fleet attacked the Asuran fleet in orbit of Asuras while McKay, Ronon, a team of marines and a Human-Form Replicator created by McKay named Fran were beamed down into the city on the planet. Fran as part of the plan absorbed all of the individual nanites to form one giant mass while McKay worked to set up the planet to detonate by overloading half a dozen ZPMs which would take out the planet and the mass while the allied fleet in orbit held off the Asuran fleet and prevented it from escaping before all the Asurans could be pulled into the mass. Unfortunately the mass started to sink into the ground and knocked out the power but by increasing the size of the mass McKay managed to cause it to sink to the planet's core causing the planet to implode destroying the planet and the mass that was made up of all of the Asurans. The combined human and Wraith fleet jumped away before the explosion. The Battle of Asuras as well as the war were over.