City Council Decision. Following the hearing by the City Council on an appealed or protested application, the City Council may affirm, reverse or modify, in whole or in part, any determination of the Planning Commission. No ordinance relating to a protested zoning or a zoning or special procedure which is contrary to a recommendation of a majority of the Planning Commission shall be adopted by the City Council only upon an affirmative vote of two-thirds (2/3) of the members of the whole City Council. In all other instances, a majority vote of the whole City Council shall be required to approve, deny or modify any recommendation of the Planning Commission with respect to a change of zoning or special procedure. A valid protest petition shall have the effect of extending the time for introduction of a bill beyond the ninety (90) day period established in Section 415.560 of this Chapter.