For weeks, Dr. Rodney McKay and a Wraith scientist later named Todd had worked on trying to create a way to shut down the Asurans. They had no success but eventually, thanks to Replicator-created clones of the First Atlantis Reconnaissance Team 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. (SGA: "This Mortal Coil", "Be All My Sins Remember'd")
At the same time, the Atlantis expedition used their ability to track the Asuran ships to evacuate the human worlds in their paths, as the Asurans 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 Asuran fleet with the new Asgard plasma beam weapons and destroyed seven out of thirty eight Asuran warships that had been built. As the Asurans were unable to discover how Atlantis was tracking them or develop a way to stop them, they recalled all of their ships to Asuras to regroup and rebuild their fleet, which they would then send out in groups. (SGA: "Be All My Sins Remember'd")
McKay and Todd were still failing in their attempts, but McKay thought up a plan to turn all of the Asuran 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 ship 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. Lt. Colonel John Sheppard managed to convince her to join the fight, who in turn managed to convince six more Traveler ships to help. (SGA: "Be All My Sins Remember'd")
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 Zero Point Modules 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. (SGA: "Be All My Sins Remember'd")
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 Dr. Rodney McKay, Ronon Dex 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 Zero Point Module's; FRAN meanwhile made her way to a room with other Asurans 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 from the Traveler's Aurora-class battleship before it could escape. During the battle, several Aurora-class battleships are destroyed by the allied fleet while more lose their hyperdrives to combined F-302 and Wraith Dart attacks. The allied fleet loses a Traveler ship and a Wraith hive ship while the Daedalus narrowly saves Todd's hive ship from destruction.
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. Colonel Samantha 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 planned. 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. (SGA: "Be All My Sins Remember'd")
With 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. (SGA: "Be All My Sins Remember'd")
Todd was able to steal several Zero Point Modules (4 of them were seen on Todd's Hive) 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 Super-hive, 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 Wraith cloning facility at the hands of Lt. Colonel John Sheppards team. The super-hive 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 Sheppard. (SGA: "Spoils of War", "Enemy at the Gate")
It was later revealed that Dr. 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. (SGA: "Be All My Sins Remember'd", "Ghost in the Machine")