The crane accident took place shortly before noon in the west suburb of Westmont, blocking the Burlington Northern Santa Fe tracks. The wreckage was cleared from the tracks around 4:30 p.m.
Earlier, Metra advised commuters who ride Metra's Burlington Northern Santa Fe railroad line to find alternative ways home Wednesday afternoon. Riders were advised to avoid Union Station entirely.
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Crews had to cut the boom from the crane truck that tipped over. They were in the process of installing a new signal bridge when something went wrong.
"They went to set the load, the crane tipped over so the boom and the bridge wound up on the main tracks," said deputy chief Jim Connolly.
Connolly says about 100 trains a day pass through the town.
They had to close the tracks on Metra's busiest line. The BNSF has 26 stops, including Naperville, Downers Grove and Aurora.
The timing of the crane collapse left many trains west of Westmont with no way to get back downtown for the evening rush hour.
Metra encouraged passengers to find alternate transportation home Wednesday night but many crowded into Union station anyway.
Even as trains started to roll through Westmont again, a little after 5 p.m., crowds remained to watch as crews tried to remove the crane.
Andy Kopale took the train downtown earlier in the day but got a ride back to the suburbs with his father.
"Otherwise I'd be with 30,000 other sweaty, smelly people at Union Station right now," Kopale said.
Metra said trains will be running behind schedule for the rest of Wednesday evening.
There is no word yet on when work on the signal lights might resume.