...or should I post this in the 'Civ3 stories' forum.
This happened to me in my last game.
I had wiped out the Aztec and the Persian. Their respective governments where still present, but they had no city anymore. So I guessed they were like 'government in exile' or so.
Suddenly, my foreign advisor told me Persia had declare war against Aztecs
Where were they fighting and why?
In the hotel hall?
Had Aztecs officials stolen the soap and towels of the Persian delegation?
The books that the world calls immoral are the books that show the world its own shame. Oscar Wilde.
I've seen similar with the Germans who I thought I'd wiped out.
It seems that if a side loses all it's cities it can still remain in existance if it has at least one Settler. A few turns later the Germans built a new 1 pop. town out in the 'No Mans Land' wilderness of unwanted land were many 'burnt' cities once stood. The Russians & French were also reluctantly colonizing this useless scrap of land and eventually killed off the remaining Germans.
I suspect something similar must have happened in your game.
'It's all just a bunch of flees fighting over who owns the dog'