The primary purpose of the line was the conveyance of passengers and goods to harbours on the Firth of Forth, from where ferries provided onward transport to locations in Fife and further afield, including northern parts of Scotland and the east coast of England.

[4] In the 1845 Parliamentary session, the E&NR had to defend hastily prepared modifications to its earlier plans, and opposition from the Edinburgh and Perth promoters was fierce.

The Edinburgh and Northern Railway was the obvious partner, and the E&NR absorbed the EL&GR by Act of 22 July 1847, taking effect on 7 August 1847.

However the work progressed well in the circumstances, and the Board of Trade inspection for passenger operation of the section from Burntisland to Cupar, and to Lindores on the Perth line, took place on 3 September 1847.

On 17 May 1848 the line was extended to another temporary terminus at Abernethy Road and on 25 July 1848 the final extension to Hilton Junction, where it joined with the newly opened Scottish Central Railway.

It was halted there while a vexatious battle took place in Parliament over the arrangement to cross, on the level or otherwise, the long-established Halbeath Railway which intersected its proposed route.

[note 7] The route for passengers from Dunfermline to Edinburgh was extremely circuitous, and this was a source of considerable friction with the railway company for many years.

Bouch saw that the proposals for hydraulic cranes at the harbours would only partly mitigate the problem, and he immediately put forward a radical scheme: what is now known as a train ferry.

At each harbour point there would be a flying bridge (as Bouch described it): this would be a large trolley system capable of running on its own rails on a ramped jetty, and carrying railway tracks.

The EP&DR Directors authorised the scheme at once, and the steamship Leviathan, 399 tons, equipped with railway track, was ready by early September 1849, but the shore works took longer.

Leviathan was a flat bottomed paddle steamer with two railway tracks aboard; a smaller vessel, PS Robert Napier, 296 tons, was constructed for the Tay passage.

The flying bridge system was nearly ready in January 1850 but there was an accident at Burntisland in which a workman was killed; the newspapers reported: The Edinburgh, Perth and Dundee Railway Company have just completed two moveable slips or platforms, one on each side of the Forth,—viz.

at Granton and Burntisland,—for the purpose of conveying across the ferry, by means of their floating railway, or large steamer Leviathan, goods, minerals, &c., without breaking bulk.

[10]A demonstration journey using the flying bridge system took place on 30 January 1850, when 12 wagons were transferred from the shore to Leviathan, followed by the Directors' in their own coach.

[1] Reports printed in contemporary newspapers differ in the details and the date: The first experimental trial took place [on the Granton to Burntisland sector] on Wednesday last [6 February 1850] in the presence of the directors, and was eminently successful.

[1] On Friday 28 March 1851, a special passenger train crossed the Forth and the Tay: [Harbour improvement works being nearly completed,] the Directors resolved to invite a number of the shareholders to be present at the formal opening of the communication between Ferry-Port and Broughty.

Friday being the day fixed upon for the ceremony, the Directors and about 300 of the shareholders accordingly started from Edinburgh at a quarter before nine o'clock morning; and having crossed the Firth in the Company's floating railway [steamship] Leviathan, proceeded, stopping at the various stations, on to Ferry-Port-on-Craig, which they reached about eleven o-clock ... On reaching Ferry-Port-on-Craig they were met by the Directors of the Dundee and Arbroath Railway, with which line a junction has now been formed at Broughty Ferry.

In order to facilitate the loading of coals ... a staith, similar to one on the Tyne, is in course of erection, by which waggon-loads will be at once discharged into the holds of vessels ...The Directors and Shareholders having gone over and examined the works, again re-entered their carriages, which were then, by means of a stationary engine, let down the inclined plain, [sic] and along a moveable platform, which can be adjusted to any level by means of a crane, so as to be attached to the deck of the large floating steam railway [ferryboat] "Robert Napier".

The rails on the platform and on the deck of the steamer being of the same gauge, and easily adjusted, the carriages, with the passengers seated, were on board in a few moments, when the large floating machine steamed out of the harbour.

There was a strong gale blowing [and an adverse tide] but the "Robert Napier" did her duty well, conveying her unusual cargo in about fourteen minutes to the other side.

The sensation of sitting in a railway carriage on board of a vessel breasting the turbulent waves was certainly a peculiar one, and the passengers generally enjoyed it.

Here, after looking at the basin, which is not quite so large as on the opposite side, although with an equal depth of water, the Edinburgh visitors were again taken on board the floating railway in the same manner as they were landed.

They were then steamed over to Ferry Port, and from thence on to the line, along which they rattled at a pleasant pace till they reached the Ladybank Junction, where they were entertained to a cold collation.

The train shortly afterwards proceeded on its way, and reached Edinburgh in safety in the afternoon ...We understand that since Friday [28 March 1851] the goods traffic has been conducted by means of the "floating railway" to and from Broughty; but it will yet be two or three weeks before the communication is thoroughly open for passengers, who, in the meantime, have to be conveyed betwixt Ferry Port and Dundee per steamer, as hitherto.

However the two ferry crossings were a liability, particularly as the rival Scottish Central Railway had a useful route from Edinburgh to Perth via Stirling, and also captured Glasgow traffic.

In subsequent days it was loaded with scrap iron to cause it to sink to a firm bed, but on 3 August 1866 the Board of the NBR sent instructions to cease work; the contractors were discharged.

[1][17] The route to Dundee from Fife was crucial to the success of the north British Railway, and despite the serious setback, it set about the construction of a second Tay bridge.

Developments had also taken place on the north side of the Tay, and the NBR had access to a through route from Dundee on to Arbroath, Montrose and Aberdeen, although much of that was jointly owned with the rival Caledonian Railway or over that company's lines by the exercise of running powers.

The original route from Burntisland to Ladybank (later connected to Wormit) was retained and continues to form part of the main line from Edinburgh to Dundee.

Dundee main line: Perth branch: Dunfermline branch: closed between Dunfermline and Townhill Junction: Gradients leaving Burntisland involved a climb for over five miles (8 km) including one mile (1.6 km) at 1 in 128; from Kirkcaldy gradients of 1 in 143, 105, 100 and 114 followed, and there was then a steep downhill run from Dysart to Thornton; from there climbing resumed at 1 in 129 and 104 to Markinch.