Ancient city crossed by ninety-nine vehicles (7)
I believe the answer is:
nineveh
'ancient city' is the definition.
(I've seen this before)
I cannot understand how the rest of the clue works.
(Other definitions for nineveh that I've seen before include "Ancient city on the Tigris" , "old city" , "Ancient Assyrian capital" , "Assyrian capital; Jonah preached against it" , "Ancient capital of Assyria" .)