The foundation for the war's final battle could be traced to its first. Scorpius ordered his command carrier to withdraw from the battle and make for Qujaga, having sensed the reemergence or received a message from the neural clone of himself that resided within the mind of John Crichton, indicating to him that the human was alive again. Believing that Crichton's wormhole knowledge might be the Peacekeepers' only hope for victory, Scorpius located the human within the hidden city on the surface of the planet. Crichton predictably refused to help his old enemy and had instead stumbled across an alternative solution: the inhabitants of Qujaga were none other than the descendants of the Eidelons, an ancient people who had once had the power to inspire peace throughout the galaxy. Learning that their ancestors included the Priests of Arnessk, Scorpius accompanied Crichton and his companions there, leaving his command carrier under Captain Braca's command in orbit of Qujaga. Following Moya's capture by the Scarrans at Arnessk, the Scarrans learned of the Eidelons' abilities. Believing them to be a threat to Scarran domination, Emperor Staleek ordered his fleet to Qujaga to wipe out the remaining Eidelons.
Staleek's personal vanguard reached Qujaga and overpowered Braca's single command carrier. Unable to defend the carrier, Braca sent a distress signal while the Peacekeepers fled the crippled ship to the Eidelons' hidden city. The late Grand Chancellor Maryk's battle group, now under command of Commandant Grayza, received the distress call. Hoping to strike a huge blow against the Scarrans by taking out its leader, Grayza ordered the fleet to assist.
The Scarrans pursued the Peacekeepers to Qujaga's surface with their own ground forces and orders to wipe out both the surviving Peacekeepers and the last of the Eidelons. The Peacekeepers attempted to hold out and defend the surviving Eidelons, but these were merely delaying tactics as the Scarrans had taken the city and were slowly but effectively wiping out isolated Peacekeepers.
A group of Luxan commandos and the Leviathan Moya soon arrived in hopes of rescuing the Eidelons. While part of the Luxan team found and safeguarded survivors, Moya's crew met up with Captain Braca's squad, who was also guarding a small group of Eidelons, in the city's main temple.
In orbit, Grayza's Peacekeeper fleet arrived and engaged the Scarrans, as did Staleek's flagship The Decimator. Both Grayza and Staleek (who believed Chancellor Maryk to still be alive) targeted each other.
On the surface, Moya's crew, the Peacekeepers, and a number of Eidelon soldiers entrenched themselves in the temple as a large force led by War Minister Ahkna assaulted their position. Though they were able to hold out for some time, the Scarrans and Charrids eventually blew a hole in the temple doors and rushed in. Close quarters fighting went on for a few minutes, before the Scarrans and Charrids were driven back and the opening barricaded. Knowing that they would not be able to repulse another attack, John Crichton led those inside the temple on a fighting retreat out of the temple toward Moya's extraction point. With air support from Luxan Kleeva Jothee's Penetrator, they successfully reached the point, but at great cost. Only a fraction of the temple's force made it, with Ka D'Argo among the casualties and Captain Braca wounded. On the Scarran side, many of Ahkna's troops were killed and Ahkna herself was dead.
In orbit, both fleets continued to battle despite suffering heavy damage on both sides. With no end in sight, Crichton, back aboard Moya, activated a wormhole weapon that had been constructed by the Leviathan's DRDs according to Crichton's specifications. The weapon created a gigantic and flame-wreathed wormhole which went unrecognized by both sides and they continued to fight even as it grew. In minutes, however, both fleets could ignore the wormhole no longer, as its size and gravitational force began to hold and pull in the armadas. Unable to escape it and facing mutual annihilation, Crichton made them an offer they could not afford to refuse: agree to end the war or let the galaxy eventually be consumed by the unstoppable wormhole. After some reluctance, both sides agreed to a cease fire and an end to hostilities.
Their assurances made, Crichton used his knowledge to destroy the wormhole, nearly costing him his own life. In the end, the fighting and the effects of the weapon had wiped out most of both fleets and ripped the planet apart.
True to their words, the battle proved to be the final of the war. Both sides ended the fighting and Grayza and Staleek met on Moya to sign a treaty overseen by Scorpius and the Eidelons, who had rediscovered their peace-inspiring abilities. The war was over.