In the City of God there
The City of God is Jerusalem.

will be a great thunder
Weather was fine in NYC

Two brothers torn apart
Terrorists and Americans are never brothers.

by Chaos, while the fortress endures
The "fortress" has hardly endured much.

the great leader will succumb
I don't think "The Great Leader" can say or spell "succumb," let alone perform it.

the third big war will begin when the big city is burning
A war; perhaps. One that will last no longer than a week.