Reil commuters were hit by delays after vandalism disrupted a number of services.
Hundreds of passengers were delayed or stranded at Bolton's railway stations due to signalling problems.
The disruption is believed to have been caused by vandals who cut cables near Farnworth station and then stole five metres of cable.
Lineside equipment was also damaged forcing trains to be halted, according to British Transport Police which is investigating the incident.
Because signals were not working train drivers had to stop trains at stations and contact signal operators from the platform for clearance to proceed. It took nine hours to repair the signals.
Fifteen trains were diverted onto other lines, a further four cancelled and 12 trains had to abort their journeys.
Many more services were delayed, according to Network Rail, with journeys between Bolton and Manchester, Blackburn and the Lake District among those affected.
Paul Cockerton, who was travelling from Manchester to his job in Blackburn, changes at Bolton station each morning. He arrived at work more than an hour later than planned.
Mr Cockerton said: "My first train was cancelled, the next was 30 minutes late and the one after that was cancelled.
"There was chaos on the platforms because we were in the dark as to what was going on. When they did arrive the trains were even more packed than normal. Hundreds of people must have been affected."
A Network Rail spokesman said: "At 1.54am on Friday problems with the signalling equipment became apparent. Once the location of the problem was found we carried out repairs and services were operating normally from 11am.
"The effect of the vandalism was that two signals in the Manchester direction and one in the Bolton direction were showing a red light, so a special method of signalling trains through the area had to be introduced.
"This ensured that trains could operate safely but the vandalism did lead to considerable disruption."
Simon Lubin, British Transport Police media relations manager, said: "Cable cutting is a significant problem which causes considerable disruption.
"It is a safety hazard to the vandals who are putting their lives at risk even in the middle of the night.
"We are investigating forensic opportunities from the incident."
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