Section 9. If the route designated in the application is agreed to by the board of aldermen or the selectmen, and all requirements in respect of the part of said route located longitudinally upon public ways and places are assented to by the directors, and thereafter are approved in writing by the department, the board of aldermen or the selectmen shall make a certificate setting forth the route as fixed by them, which shall be certified by said board or their clerk to the directors, and no further proceedings shall be necessary, but the route so agreed to shall be the route of said railroad in such city or town, except as hereinafter provided. The fee for such a certificate shall be set by the board of aldermen or the selectmen. If the board of aldermen or the selectmen agree with the directors upon a route different from that designated in the application, or fail within ninety days after the date of the filing of the application to agree with the directors upon a route, or as to requirements in respect of the part of the route located longitudinally upon public ways and places which meet with the approval of the department, the directors or the board of aldermen or selectmen, within one hundred days after the date of the filing of the application, may apply to the department, which may, in its discretion, after notice to the directors and board of aldermen or selectmen, and after public notice and a hearing, fix the route and determine the grades and method of constructing said railroad in such city or town, and no change shall thereafter be made by the directors in the grades or method of construction so determined without the written approval of the department after notice to the board of aldermen or selectmen and after public notice and a hearing. The department shall thereupon make a certificate setting forth the route as fixed by it, which route shall be certified by its clerk to the directors. In fixing such route the department shall not locate it longitudinally upon any public way or place in such city or town without the consent of the board of aldermen or the selectmen. That part of the route consisting of a location longitudinally upon a public way or place shall not be deemed to be fixed until all requirements imposed in respect of it by the board of aldermen, or the selectmen, are approved in writing by the department. If the route in any city or town, as fixed either by the board of aldermen or selectmen, or by the department, in the manner hereinbefore provided, is different from the route designated in the application of the directors and if said change of route in the opinion of the directors makes it desirable to change the route of said railroad in any of the other cities or towns through which the route of said railroad passes, or if the directors deem it desirable to change the route of the railroad so as to pass through any cities or towns not named in the agreement of association of said railroad company or to change the route so as no longer to pass through certain cities or towns where the directors have applied to have the route fixed, then the directors may at any time before the route in all the cities and towns is finally fixed, or within thirty days thereafter, apply to the department for leave to apply again to the board of aldermen or selectmen of any cities or towns to fix a new route other than that originally applied for within such cities or towns or to apply to the board of aldermen or selectmen of any cities or towns not named in the agreement of association of said railroad company to fix a route of the railroad passing through such cities or towns, or for leave to abandon the route in any cities or towns where the directors have applied, as aforesaid, to have the route fixed. With such application to the department the directors shall file a map and general profile showing the change in the route as proposed, which map and general profile shall be in the same form as those filed under section seven, and the directors shall also furnish such additional information as the department may require. The department shall give a public hearing upon such application after giving such notice to the directors and to the board of aldermen or selectmen of such cities or towns as it deems requisite. If the department authorizes the directors to apply to any cities or towns to fix a route other than that designated in the original application, then all proceedings theretofore taken in regard to fixing the route in such cities or towns shall become null and void, and the directors shall, within sixty days thereafter, again apply to the board of aldermen of such cities and to the selectmen of such towns to fix anew the route of the railroad in such cities or towns, and with such application shall file a copy of the maps and general profile of such proposed altered route, and, upon request, the other information presented to the department. The proceedings thereafter upon such application shall be as provided for an original application. If the department authorizes the directors to apply to any cities or towns not named in said agreement of association to fix a route of the railroad passing through said cities or towns, then the directors shall, within sixty days after the granting of such authority, apply to the board of aldermen or selectmen to fix the route of the railroad in such cities or towns. Said application shall be made in the same manner and the proceedings thereon shall be the same as in an application to fix the route of the railroad to the board of aldermen or selectmen of a city or town originally named in the agreement of association of such railroad company. If the department authorizes the directors to abandon entirely the route in any cities or towns where the directors have applied, as aforesaid, to have the route fixed, then any action taken in regard to fixing the route in such cities or towns shall become null and void, and the railroad company shall be under no obligation to construct its railroad therein. The order of the department authorizing the directors to apply for a route of the railroad in any city or town not named in the agreement of association or the order of the department under which the route in any cities or towns is abandoned, shall operate as an amendment to the clauses in said agreement of association which name the cities or towns where the railroad is to be located, and the termini thereof, and a certified copy of said order shall be attached to the agreement of association.