, Exile a creature you control: Put a storage counter on this land.
: Add for each storage counter on this land.
You can activate City of Shadows's second ability while it has no storage counters on it, though it won't add any mana 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.
, 
for each storage counter on this land.