The huge project overran and cost far more than planned, but passengers can expect more services and faster journeys

It has come years late, with bits missing and at double the price. But a landmark moment in one of rail’s most costly and controversial sagas, the Great Western mainline upgrade, may still give cause for appreciation this week, when an Inter City Express train carries passengers for the first time along an electrified section of the route.

The train and, in particular, the electrified track, have had a long and painful genesis: interlinked projects costing billions more than originally planned. The idea to purchase bi-mode trains, able to run on diesel and electricity, was conceived by the Department for Transport a decade ago, leading to a new Hitachi assembly plant in Britain rolling out Class 800 trains.

Just over £4bn of these new trains are destined for Great Western. Extra costs of about £300m were incurred by the DfT in storing them while electrification of the track stumbled slowly on.

Network Rail chiefs, dragged in front of the public accounts committee, had to confess that the £874m quoted to electrify the line would rise to £2.8bn. Ministers later decided it would never get further west than Cardiff, nor, probably, into the city centres of Bristol, Oxford and Bath. And electrification was only half the overall bill for modernising the route.

So what do you get for your £10bn and why did it cost so much? The full benefits may not be immediately apparent to the lucky passengers riding the first train this week, bar promised extra legroom. The electricity is only on as far as Maidenhead for now, but by the start of 2019, when the full fleet of 57 trains has entered service and the line is electrified to Cardiff, journeys will be up to 17 minutes faster from Bristol to London, and more services will run. Trains will have up to 652 seats, almost 100 more than the longest ones now.

Underpinning the greater capacity should be more reliable infrastructure, smoothing the path for quieter, greener trains. If its reputation for accounting has been shredded, Network Rail expects to show that it has nonetheless significantly transformed the railway, in a project where difficulties have extended far beyond engineering.

Issues to beset the work ranged from driving piles through signalling cables to negotiating permission to dislodge multiple endangered species and listed buildings. On a special Network Rail observational train running from London Paddington to Swindon earlier this week, Mark Carne, the chief executive of Network Rail, was candid about the failures but defiant as to the challenge.

Carne still quotes the conclusion of the accounts committee chair that Great Western was “a stark example of how not to run a major project”. But from here, the scale of what has been transformed becomes clearer: not just electrified tracks, but a remodelling of crucial intersections.

The rebuilding of Reading station, adding platforms and unpicking some of the intersecting tracks around it, has been obvious to passengers; less so, perhaps, the flyovers and dive-unders constructed at Stockley and Acton to avoid delays to express passenger services by freight wagons or trains crossing to Heathrow.

Even what is counted as electrification has involved not just putting up wires but a host of engineering works around the tracks. The core of electrification has meant about 7,000 masts being erected along the route: each site requiring 10 visits by engineers to dig holes, lay foundations, drive in steel masts, and fit booms, girders and wiring.

For each of those visits, Carne said, the most challenging thing has been “to enter and leave the work site every night and keep the railway running”.

Most nights, that would only mean a gap of about four-and-a-half hours without trains running on the route, which is heavily used by freight trains as well as passenger services.

“In that time, we’ve got to bring the kit in, and every time we finish, the railway has got to be completely functional,” he said.

Miles of work has been carried out in tunnels, depots and substations have been built, and about 160 bridges have been altered or replaced along the way. While engineers should be able to calculate how long demolition, design and rebuilding will take, planning consents are less controllable.

One bridge remains uncrushed, due to an unresolved planning dispute in Oxfordshire. The regular steel frames of electrical masts on the trains will disappear for about 1,600ft (490 metres) at Steventon. The Grade II-listed bridge is too low for wires, but remains standing due to the opposition of residents dismayed at the prospect of a key road closing for 10 months, leaving Network Rail with a tantalising missing piece.

That row means that when the otherwise fully electrified mainline opens in 2019, drivers will need to lower the pantograph, the part of the train that connects it to the electrical power supply line, when they approach Steventon bridge.

This could mean trains effectively freewheeling along the track until they can reconnect on the other side. Carne’s frustration is evident: “We’re now going to slow down every train to get under that bridge, because we can’t get permission. These things add up.”

Performance has been under scrutiny from the government, with rail funding having been announced on Thursday for the five years from 2019, a direct grant of £35bn and potential overall budget of up to £48bn. The caveat is that funds for major upgrades will now not be allocated in advance and could go to competing contractors, rather than Network Rail.

By the time those negotiations come around, Carne will hope that the benefits of Great Western, rather than the costs, will be at the forefront. This weekend, emergency engineering works will close the line around Reading, but Carne points out that for most of the time, services have continued to run as normal, unlike during much of the similarly ruinous West Coast upgrade.

“We’ve maintained that while completely transforming it. It’s such a major artery, you’ve just got to keep it flowing,” he said.