The transit agency initially issued an alert at about 10:10 a.m. about the problem, which shut down all stations between Hayward and Berryessa/North San Jose. Those stations have since reopened.
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Before noon, service was restored at three of the stations furthest South, Warm Springs, Milpitas and Berryessa in North San Jose. The Hayward, South Hayward, Union City and Fremont stations remained closed.
"We see like almost all the gates are closed and people are just exiting and so we asked (an employee), 'Oh, what's going on?' They're like, 'Oh, the buses, the trains are shut down something happened in the computers," said passenger Mike Lee from San Jose.
BART officials told ABC7 that its system experienced a network computer shutdown.
"One of the reasons we're not running trains is out of that abundance of caution for safety," said BART spokesperson Chris Filippi. "Whenever anything impacts the train control system, that requires us to respond and to be assured that it's working properly because that system is what allows us to avoid any sort of, collisions on the system."
This latest issue comes almost two weeks after an electrical fire that forced several BART stations to close in Oakland.
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Ripple effects from those closures caused delays in service that lasted for days after.
"It does appear to be separate issues, but certainly any time that we provide service that is not reliable and not what our riders are typically expecting, that's a disappointment for us as much as them," Filippi said.
Passengers impacted by the latest shutdowns were encouraged to find other transportation and also offered alternatives.
"There is mutual aid from both AC Transit and VTA, which means they are honoring BART fare," Filippi said. "And there is also a bus bridge, an additional bus bridge that's been set up thanks to AC Transit. So we have more buses than usual operating between those stations to try to help people."
Still, for many of the passengers, it's been a frustrating day.
"I was coming out going out to go visit family," Lee said Thursday. "So there is a chance I might not be able to today and I might have to just do it till tomorrow. It is a bit of an inconvenience. The real inconvenience for me is more of, I had to come from the other side of town to get here."