I'm not entirely clear from your question who is violating the zoning ordinance or what relief you are seeking. My assumption is that the business you are operating as a tenant is in violation of a zoning ordinance. It is unclear if any government agency has taken or threaten to take action against you. If you are in violation, the first step is to look at your lease for a provision called "Compliance with Laws" or something similar. A "Compliance with Laws" provision in a commercial lease requires the tenant to comply with all applicable local, state, and federal laws and regulations. This can cover a wide variety of laws, such as zoning laws, environmental regulations, public health requirements, building codes, occupational safety rules, etc. This provision would typically shift the responsibility for compliance to you, the tenant.
This clause might look something like this:
"The Tenant will, at the Tenant's own cost and expense, comply with all of the statutes, bylaws, rules, regulations, orders and decisions of any and all governmental authorities having jurisdiction and all bodies involved with the enforcement thereof relating to the premises, the use and occupancy thereof, and the sidewalks, curbs, vaults, vault spaces, and streets adjacent thereto."
Failure to comply with this clause could be grounds for the landlord to terminate the lease and evict you. You could be liable for damages to the landlord for violating the lease.
In terms of your options, as I mentioned review the lease to see who is responsible. If the lease is silent, and the landlord made certain representations to you regarding your ability to operate, it is possible that the landlord is responsible. Also, depending on the relief you seek, you may be able to negotiate a lease termination and avoid a lawsuit against you. Finally, you may be able to get a zoning variance to allow you to operate as you initially intended.
I would recommend speaking to an attorney as soon as possible. To talk to our real estate team, please contact us at (303) 688-0944 for a free consultation. The specific facts will determine the best course of action in your case.