Rail passengers on the East Coast mainline faced disruption chaos after lightning strikes damaged signalling.
London North Eastern Railway (LNER) advised passengers not to travel on Friday "due to the extreme weather conditions and signalling failure".
Trains are now running but some are delayed, with others being cancelled.
British Transport Police said officers had to hold back passengers trying to get on platforms at Leeds station.
Dan Wales, 26, was stuck at the station for more than three hours trying to get home to Newcastle.
He said he had "been told by staff that unless you're going to London or Manchester, don't expect anything".
A number of trainee teachers attending a Teach First conference in Leeds were also stranded by the disruption.
About 1,300 people were due to leave on Friday, with many planning on taking the train.
Teach First said people were being urged to remain at Leeds University and check before travelling to the station.
A spokesman said: "The Student's Union and Refectory at Leeds University are open and we are working with the university on contingency plans if anyone is unable to travel today."
At 16:45 BST, LNER said all lines had re-opened, with services running the full routes in both directions between London King's Cross and Edinburgh, and King's Cross and Leeds.
However, the operator said services were still "subject to change and delay" and disruption would continue until the end of the day.
LNER said ticket restrictions had been lifted so passengers could travel on alternative routes or at a later date.
Network Rail said although services were running from Leeds, schedules had been significantly affected and passengers should check before travelling.
It said it did not have the figures for how many people were affected by the disruption but said it was a "significant number".
Train operator Northern, who operate a majority of local services in Yorkshire, said: "Customers are asked to check carefully before travelling later in the afternoon as services are likely to be subject to further delays and cancellations."
Other operators TransPennine Express and Cross Country services have also been affected, with passengers being urged to check before they travel.
Cross Country warned customers of delays and alterations to its services after "a fault with the signalling system" at March, near Peterborough, which had left train lines blocked in both directions.
The signalling centre in York was also hit by lightning strikes.
Commuter Helen King had her journey to Leeds from Apperley Bridge halted, saying she was "back where she started after an hour and 25 minutes".
She added: "The train staff kept us as updated as they could, after half an hour they informed us of our right to compensation which didn't do much to placate those who just wanted to get into Leeds.
"Finally after an hour of standstill the driver announced that he had been told to turn the train around and head back to Bradford."
Another passenger Barry Lee was travelling from Newcastle to York when people were told to leave the train at Darlington "due to a lightning strike at York station which had a severe affect on signalling".
"We were told to get off the train, which then headed back to Newcastle," he said.
Commuter David Renwick tweeted that severe thunder and lightning had struck and said the information boards were off at York railway station.
Severe thunder and lightning at York Train Station, struck roof and all the information boards off! Huge collective jump from everyone waiting! Journey could be interesting! pic.twitter.com/8IYFkFDmBK— David Renwick (@dave_renwick) July 27, 2018
UPDATE: Lines have reopened at #March following a fault with the signalling system. Delays and alterations will still occur while services recover.— CrossCountry trains (@CrossCountryUK) July 27, 2018
LNER, which runs services on the East Coast route after the franchise operated by Stagecoach and Virgin Trains failed, tweeted that tickets for Friday would be valid on the weekend.
#LNERUpdate Due to the extreme weather conditions and signalling failure throughout the route our advice to passengers is as follows:— London North Eastern Railway (@LNER) July 27, 2018
Do not travel today (27/07/2018)
Tickets will be valid for tomorrow (28/07/2018) and Sunday (29/07/2018).
But it was criticised by stranded passengers who said "people have places to be".
How can you give this advice??? People have places to be things to do. We can’t just delay by a day or two. Have some respect for paying passengers and find a real solution. This weather has been expected all week.— Jonathan Ellis (@Jonathan__Ellis) July 27, 2018
Yes but given some people are already TRAVELLING advice not to travel is useless. What practically are we advised to do? Get off at Newcastle and get a hotel?— HillsideSaint1988 (@HSaint1988) July 27, 2018
Bursts of torrential rain crossed parts of Yorkshire on Thursday night, as hailstones bounced off cars and roads.
On Friday morning areas across North Yorkshire were hit by lightning strikes.
Fire crews were called to homes hit by lightning in Nether Poppleton, Wiggington, and Carrfield in York.
The homes were damaged by the strikes, but there are no reports of injuries.
Please include a contact number if you are willing to speak to a BBC journalist. You can also contact us in the following ways: