- "We need to take the Asurans out while they're all in one place, and we need to do it quickly."
- —Samantha Carter
- "Just give me and the Wraith, like, ten hours to get this shut-down program working. If I don't, then you can just feel free to go ahead and open up on ‘em with your beam weapons."
- —Rodney McKay
For weeks Dr. Rodney McKay and a Wraith scientist later named Todd had worked on trying to create a way to shut down the Replicators. They had no success but eventually, thanks to Replicator-created clones of Atlantis 1 and Dr. Elizabeth Weir, they gained the ability to track Asuran Aurora-class ships and summoned the newly upgraded Apollo and the Daedalus to deal with them. 
At the same time, the Atlantis Expedition used their ability to track the Replicator ships to evacuate the human worlds in their paths, as the Replicators had begun destroying all human worlds they came across as part of a strategy in their war with the Wraith in an attempt to starve them. The Apollo and the Daedalus began ambushing the Replicator fleet with the new weapons given to them by the Asgard and destroyed seven out of thirty eight Asuran warships that had been built. As the Asurans were unable to both discover how the Atlantean ships were tracking them and develop a way to stop them, they recalled all of their ships to their homeworld to regroup and rebuild their fleet, which they would then send out in groups. 
McKay and Todd were still failing in their attempts, but McKay thought up a plan to turn all of the Replicators into a super-dense blob of nanites that would render them essentially inert. However, in order for this plan to work every single Asuran needed to remain in orbit long enough for the mass to grow large enough to pull them in. The Daedalus and the Apollo, powerful as they were, could not hope to hold off the Asuran fleet that long, and so the Expedition asked the Wraith for help. Using Todd to negotiate, they managed to obtain seven hive-ships willing to fight with the Tau'ri side-by-side to destroy the Asurans once and for all.
On the way back to Atlantis, the team encountered the Aurora-class ship commanded by Larrin of the Travelers. Sheppard managed to convince her to join the fight, who in turn managed to convince six more Traveler ships to help. 
On Atlantis, McKay created a human-form Replicator named FRAN, who informed him that the mass they will be creating will be able to regain control of itself far sooner than originally expected. To counter the problem FRAN proposed overloading the ZPMs around the mass, which would implode the mass and destroy the planet and orbiting fleet in the process. After ironing out the details, the Daedalus, the Apollo and the Traveler's Aurora-class battleship meet up with the Wraith and Traveler fleets. The allied fleet then jumped into hyperspace on a course for Asuras. 
- "I don't wanna be doing this all day."
- —Steven Caldwell
The combined human and Wraith fleet arrived in orbit over Asuras and immediately opened fire, catching the Asurans off guard and destroying a handful of their ships in the process. The Apollo beamed McKay, Ronon and a team of marines into the Core Room, while FRAN was beamed into one of the city's many corridors. McKay interfaced with the core and took control of the city's power grid in order to overload the city's ZPM's; FRAN meanwhile made her way to a room with other Replicators in it.
In space, the allied fleet successfully held off the Asuran fleet, and the Asurans never seemed to figure out the real objective of the assault. FRAN activated the program McKay installed in her, causing every nanite on the planet to be attracted to her, fusing together to the point where they began creating a mass with a neutron star level of density. An Asuran battleship tried to jump into hyperspace but Sheppard destroyed it with a salvo of drone weapons (only two impacted, the rest were intercepted by other drones before impact) from the Traveler's Aurora-class battleship before it could escape.
The nanite mass eventually grew large enough to pull the nanites in orbit into the mass, but before McKay could overload the ZPMs the mass grew so heavy that it began to sink into the planet, collapsing the subterranean power grid and causing a blackout throughout the city, preventing the ZPMs from overloading. Carter, using the Daedalus' sensors, detected that the planet's surface was rich with neutronium, the building block of the nanites and an incredibly dense material.
Using this data, it was determined that if the mass absorbed the neutronium around it, it would become so heavy that it would sink into the planet's core, where the pressure would cause the mass to implode. With a few minor adjustments from McKay, the blob absorbed the neutronium and sunk into the planet's core as planed. McKay, Ronon and the team of marines were beamed aboard the Daedalus and the allied fleet jumped into hyperspace just before the planet exploded, taking the Replicator mass and their fleet with it. 
- "We can finally get to work without having to look over our shoulders. It's time to begin."
- —Replicator WeirWith the destruction of the Asurans, the Asuran-Tau'ri-Wraith war came to an end, but so did the truce between the Tau'ri and the Wraith, resulting in a resumption of hostilities by both sides. The Travelers, meanwhile, became permanent allies of the Expedition. 
Todd was able to steal several ZPMs from the planet before it was destroyed, planning to use three to power the Wraith cloning facility which had turned the tide of the Lantean-Wraith war and create an army which he could use to conquer the other Wraith factions. A number of others were given to his best scientists to try and create a ZPM-powered hive-ship, a project that would last for well over a year; still more were hidden away for future use. Todd's plan to create a clone army was quickly interrupted when a Wraith under his command betrayed him, triggering a series of events which eventually led to the destruction of the cloning facility at the hands of Atlantis 1. The ZPM-powered hive-ship was eventually made a reality, but one of the project's scientists mutinied and took control of the ship. It was eventually destroyed over Earth by a nuke planted by John Sheppard. 
It was later revealed that Elizabeth Weir and a small group of Asurans had survived aboard an Aurora-class battleship. They were all that remained of Niam's faction, and were still seeking ascension. Until the Battle of Asuras was fought they were being hunted by the Asurans for their beliefs, and so were not present during the battle. They had little hope of surviving until they learned that Asuras and the Asurans had been completely wiped out, allowing them to strive for ascension in peace.