I've been doing some digging on this and I saw people saying that it was bombed with a Thermobaric Missile that didn't wipe out the whole city like a nuke would have. The reference for this came from an interview with Capcom writer Yasuhisa Kawamura:
Q19. What kind of missile appear in the ending?
A19. Second to nuclear bombs in power, it is one new type of bomb like a thermobaric bomb. Details are unknown, but its radioactive contamination seems to be extremely low. In this story, it could be said that it is, along with the rail cannon, a top-secret weapon of the US military.
In 1999 Famitsu and Studio Bentstuff interviewed Capcom writer Yasuhisa Kawamura, who answered questions regarding the story of Resident Evil 3: Nemesis.
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