Freedom did not go nuclear then or ever. It even clearly showed in the very next episode that Kira had hit the "Emergeny Shut Off" for the nuclear reactor. That huge explosion was the matter/anti-matter reaction when the Tannhauser (Minerva Positron Cannon) hit the ocean's surface while trying to get Archangel. You can even see when that explosion is approaching the Minerva it was facing it and the red line from the after effect of firing the Tannhauser was still there as it began to turn away from the explosion.Originally posted by: SkyReaper
Well, when Impulse put his sword through Freedom, it breached his reactor making it go nuclear.