Initially receiving a favourable reception, the company brought in several service alterations and innovations, including the leasing of Class 373 Regional Eurostars along with the refurbishment of the InterCity 225 fleet.

Plans to procure a fleet of tilting trains based on the Pendolino were mooted by the company, but were discarded amid a protracted and complex refranchising process.

Following its inability to fulfil agreed payments, GNER was stripped of the franchise during December 2006, although it continued to run services on the route for another year via a management contract.

The final northbound GNER train was the 20:30 London King's Cross – Newcastle on 8 December 2007; the company was replaced by the new franchisee National Express East Coast one day later.

[2] During January 1997, Sea Containers Chairman James Sherwood announced that GNER intended to procure a pair of two new-build tilting trains; these were claimed to enable the London-Edinburgh journey to be reduced to only 3 hours and 30 minutes, in part achieved via their increased maximum speed of 140mph (225kmh).

[2] According to Rail magazine, the operator's customer service was frequently praised, while passengers also warmed received its promises of an increased quality of onboard catering.

On 17 October 2000, the Hatfield crash occurred with the high speed derailment of an Intercity 225 set, which was primarily caused by the failure of a rail that had been poorly maintained.

[2] The incident had deeply affected GNER’s business, not only due to a significant drop in confidence amongst its passengers but the rapid enactment of many emergency speed restrictions imposed by the national infrastructure company Railtrack.

[6] GNER's submission had included its plan to purchase a fleet of 25 tilting trains, similar to the British Rail Class 390 Pendolinos then being introduced on the West Coast Main Line; this were envisioned to feature multiple types of propulsion, being divided between electric and diesel-powered examples so that they could serve all of the franchise's destinations.

[2] However, in January 2002, the Strategic Rail Authority announced that the refranchising process had been scrapped and that a two-year extension had been awarded to Sea Containers, extending GNER's franchise period to April 2005.

[10][11] The terms of the new franchise had considerable differences from that of the original period; instead of GNER receiving subsidies for its operations, it would be instead paying the British state for the privilege of doing so; there was reportedly concerns over the financial viability of such an arrangement from the onset.

The company rejected this assertion, stating that its lines of credit and financial activities were "ring-fenced" away from Sea Containers, and therefore a cessation of services for this reason was impossible.

It did not however stop speculation from rival TOCs (principally First) and Virgin Rail Group that they would be keen to rebid for the ECML franchise if it were put back out to tender.

In July 2006, rumours began circulating that Sea Containers would be prepared to sell GNER in an effort to stave off resorting to Chapter 11 proceedings to secure itself from its creditors.

[citation needed] That same month, GNER announced that its chief executive officer, Christopher Garnett, was to step down, having occupied that position since Sea Containers had originally been awarded their first franchise.

Amid growing industry speculation that Sea Containers was working towards a "financial restructuring", the company's President and Chief Executive Bob Mackenzie was named as Garnett's successor.

[14] The firm's problems were further fuelled by GNER's poor profitability, which had been linked to the company's overbidding for the franchise coupled to what proved to be crippling premium repayments to the government.

The company attempted to address the problem by waiving booking fees on internet sales, cutting staff numbers, and raising fares and car-parking charges where the market could bear it.

[2] During December 2006, the Department for Transport announced its intention to strip Sea Containers of its franchise; this was reportedly due to the company's financial issues and having been overbid.

[2] In February 2007, the Department for Transport announced that Arriva, FirstGroup, National Express and Virgin Rail Group had been shortlisted to lodge bids for the franchise.

Other towns and cities served by GNER trains included Stevenage, Peterborough, Grantham, Newark, Retford, Doncaster, Wakefield, Shipley, Keighley, Horsforth, Brough, York, Northallerton, Darlington, Durham, Newcastle, Morpeth, Alnmouth (for Alnwick), Berwick-upon-Tweed, Dunbar, Motherwell, Inverkeithing, Kirkcaldy, Leuchars, Arbroath, Montrose, Stonehaven, Falkirk, Stirling, Perth, Pitlochry, Kingussie, and Aviemore.

With the completion of the Allington Chord, near Grantham, having increased track capacity, GNER began to operate a full half-hourly service throughout the day on this route in May 2007.

The trains leaving King's Cross on the half-hour generally terminated at Newcastle and served other intermediate stations such as Grantham, Newark, Retford, Doncaster and Durham as well as Peterborough, York, and Darlington.

[2] By 2000, it was clear that GNER's Class 91 fleet was in need of refurbishment to address reliability issues, thus the company made arrangements to lease alternative traction as a stop-gap measure.

This ambition was expanded in the early 2000s when, as part of a refranchising bid, GNER stated that its planned to purchase a fleet of 25 tilting trains, similar to the British Rail Class 390 Pendolinos then being introduced on the West Coast Main Line; this were envisioned to feature multiple types of propulsion, being divided between electric and diesel-powered examples so that they could serve all of the franchise's destinations.