{T}, Exile a creature you control: Put a storage counter on City of Shadows.
{T}: Add {C} for each storage counter on City of Shadows.
You can activate City of Shadows’s second ability while it has no storage counters on it, though it won’t add any mana to your mana pool in this case. You did not tap it for mana, though, in case any abilities (such as the ability of a Fertile Ground enchanting it) care about that.
The storage counters aren’t removed when you activate the mana ability.